SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 7NHF | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | MICROFLUIDIC | 7 | 294 | 600 mM Sodium citrate and 100 mM HEPES pH 7 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.99 | 58.86 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 180.3 | α = 90 |
| b = 180.3 | β = 90 |
| c = 119.2 | γ = 120 |
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | PIXEL | PSI JUNGFRAU 4M | | 2023-01-26 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.07 | ESRF | ID29 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | SOS Chip | fixed target |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | 20635 | 20827 | 20635 | |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 2.5 | 94.75 | 100 | 0.96 | 5 | 44.2 | | 50011 | | | 45.27 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.5 | 2.54 | 100 | | 0.27 | 0.8 | 44.2 | |
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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.5 | 65.396 | 50003 | 2510 | 99.984 | 0.16 | 0.1584 | 0.17 | 0.1883 | 0.19 | 59.187 |
| 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] |
|---|
| 0.006 | 0.003 | | 0.006 | | -0.02 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 14.633 |
| r_dihedral_angle_6_deg | 14.104 |
| r_lrange_it | 11.962 |
| r_lrange_other | 11.951 |
| r_scangle_it | 9.728 |
| r_scangle_other | 9.702 |
| r_dihedral_angle_2_deg | 9.081 |
| r_mcangle_it | 7.523 |
| r_mcangle_other | 7.523 |
| r_dihedral_angle_1_deg | 6.5 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 14.633 |
| r_dihedral_angle_6_deg | 14.104 |
| r_lrange_it | 11.962 |
| r_lrange_other | 11.951 |
| r_scangle_it | 9.728 |
| r_scangle_other | 9.702 |
| r_dihedral_angle_2_deg | 9.081 |
| r_mcangle_it | 7.523 |
| r_mcangle_other | 7.523 |
| r_dihedral_angle_1_deg | 6.5 |
| r_scbond_it | 6.193 |
| r_scbond_other | 6.109 |
| r_mcbond_it | 4.956 |
| r_mcbond_other | 4.956 |
| r_angle_refined_deg | 1.511 |
| r_angle_other_deg | 0.504 |
| r_nbd_refined | 0.206 |
| r_symmetry_nbd_other | 0.195 |
| r_nbtor_refined | 0.168 |
| r_nbd_other | 0.162 |
| r_symmetry_nbd_refined | 0.14 |
| r_xyhbond_nbd_refined | 0.135 |
| r_symmetry_xyhbond_nbd_refined | 0.107 |
| r_symmetry_nbtor_other | 0.079 |
| r_ncsr_local_group_3 | 0.078 |
| r_ncsr_local_group_6 | 0.075 |
| r_chiral_restr | 0.072 |
| r_ncsr_local_group_5 | 0.07 |
| r_ncsr_local_group_2 | 0.063 |
| r_ncsr_local_group_1 | 0.06 |
| r_ncsr_local_group_4 | 0.059 |
| r_bond_refined_d | 0.006 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | 0.001 |
| r_gen_planes_other | 0.001 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 8088 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 186 |
| Heterogen Atoms | 72 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| MOLREP | phasing |