SSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batch conditions
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 | BATCH MODE | 7 | 294 | 600 mM Sodium citrate and 100 mM HEPES pH 7 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.86 | 57.05 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 177.9 | α = 90 |
| b = 177.9 | β = 90 |
| c = 117.3 | 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 | 19325 | 20268 | 19325 | |
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 | 93.33 | 100 | 0.96 | 4.4 | 47.4 | | 47878 | | | 49.36 |
| 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 | | 0.17 | 0.5 | 45.18 | |
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) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.5 | 64.472 | 47873 | 2316 | 99.994 | 0.169 | 0.1676 | 0.18 | 0.1934 | 0.2 | RANDOM | 59.434 |
| 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] |
|---|
| -0.005 | -0.002 | | -0.005 | | 0.016 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 15.18 |
| r_dihedral_angle_6_deg | 14.129 |
| r_lrange_other | 11.013 |
| r_lrange_it | 11.006 |
| r_scangle_it | 9.179 |
| r_scangle_other | 9.099 |
| r_dihedral_angle_2_deg | 7.892 |
| r_mcangle_it | 6.57 |
| r_mcangle_other | 6.57 |
| r_dihedral_angle_1_deg | 6.304 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 15.18 |
| r_dihedral_angle_6_deg | 14.129 |
| r_lrange_other | 11.013 |
| r_lrange_it | 11.006 |
| r_scangle_it | 9.179 |
| r_scangle_other | 9.099 |
| r_dihedral_angle_2_deg | 7.892 |
| r_mcangle_it | 6.57 |
| r_mcangle_other | 6.57 |
| r_dihedral_angle_1_deg | 6.304 |
| r_scbond_it | 5.847 |
| r_scbond_other | 5.714 |
| r_mcbond_it | 4.34 |
| r_mcbond_other | 4.339 |
| r_angle_refined_deg | 1.407 |
| r_angle_other_deg | 0.458 |
| r_nbd_refined | 0.213 |
| r_symmetry_nbd_other | 0.199 |
| r_nbtor_refined | 0.173 |
| r_symmetry_nbd_refined | 0.157 |
| r_nbd_other | 0.152 |
| r_symmetry_xyhbond_nbd_refined | 0.141 |
| r_xyhbond_nbd_refined | 0.135 |
| r_symmetry_nbtor_other | 0.082 |
| r_ncsr_local_group_5 | 0.07 |
| r_ncsr_local_group_6 | 0.07 |
| r_ncsr_local_group_3 | 0.064 |
| r_chiral_restr | 0.062 |
| r_ncsr_local_group_1 | 0.062 |
| r_ncsr_local_group_2 | 0.061 |
| r_ncsr_local_group_4 | 0.059 |
| r_bond_refined_d | 0.005 |
| r_gen_planes_refined | 0.004 |
| r_bond_other_d | 0.001 |
| r_gen_planes_other | 0.001 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 8056 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 181 |
| Heterogen Atoms | 20 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| MOLREP | phasing |