Human NOQ1 enzyme in complex with NADH by serial crystallography
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 8RFN | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 8.5 | 293 | 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 20% polyethylene glycol (PEG) 3350 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.58 | 52.41 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 61.06 | α = 90 |
| b = 106.79 | β = 90 |
| c = 196.01 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 295 | PIXEL | PSI JUNGFRAU 4M | | 2023-02-18 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.072 | ESRF | ID29 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
| Fixed Target |
|---|
| Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
|---|
| 1 | small SOS chips | | | | | |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
|---|
| 1 | 2.7 | 98 | 100 | 0.154 | 7.6 | 154.1 | | 32476 | | | 75.6 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.7 | 2.77 | | | 0.976 | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.7 | 98 | 32476 | 3618 | 99.98 | 0.20283 | 0.19848 | 0.21 | 0.24254 | 0.25 | RANDOM | 65.395 |
| Temperature Factor Modeling |
|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
|---|
| -0.05 | | | 0.09 | | -0.04 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 15.893 |
| r_long_range_B_refined | 10.494 |
| r_long_range_B_other | 10.494 |
| r_scangle_other | 7.848 |
| r_mcangle_it | 7.429 |
| r_mcangle_other | 7.428 |
| r_dihedral_angle_2_deg | 7.346 |
| r_dihedral_angle_1_deg | 6.797 |
| r_scbond_it | 4.936 |
| r_scbond_other | 4.936 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 15.893 |
| r_long_range_B_refined | 10.494 |
| r_long_range_B_other | 10.494 |
| r_scangle_other | 7.848 |
| r_mcangle_it | 7.429 |
| r_mcangle_other | 7.428 |
| r_dihedral_angle_2_deg | 7.346 |
| r_dihedral_angle_1_deg | 6.797 |
| r_scbond_it | 4.936 |
| r_scbond_other | 4.936 |
| r_mcbond_it | 4.788 |
| r_mcbond_other | 4.787 |
| r_angle_refined_deg | 1.178 |
| r_angle_other_deg | 0.396 |
| r_chiral_restr | 0.054 |
| r_bond_refined_d | 0.005 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | 0.001 |
| r_gen_planes_other | 0.001 |
| r_dihedral_angle_4_deg | |
| r_nbd_refined | |
| r_nbd_other | |
| r_nbtor_refined | |
| r_nbtor_other | |
| r_xyhbond_nbd_refined | |
| r_xyhbond_nbd_other | |
| r_metal_ion_refined | |
| r_metal_ion_other | |
| r_symmetry_vdw_refined | |
| r_symmetry_vdw_other | |
| r_symmetry_hbond_refined | |
| r_symmetry_hbond_other | |
| r_symmetry_metal_ion_refined | |
| r_symmetry_metal_ion_other | |
| r_scangle_it | |
| r_rigid_bond_restr | |
| r_sphericity_free | |
| r_sphericity_bonded | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 8946 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 17 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| MOLREP | phasing |