Human Gamma-D Crystallin R36S fresh serial crystallographic structure
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1HK0 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 7.8 | 298 | 50 mM phosphate buffer pH 7.8, 20 mM DTT |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.58 | 52.41 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 53.6 | α = 90 |
| b = 83.7 | β = 90 |
| c = 100.4 | 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 | 298 | PIXEL | DECTRIS PILATUS 6M | | 2021-09-29 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.99 | Diamond | I24 |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 2.1 | 38.66 | 99.9 | 0.974 | 0.19 | 3.87 | 26.7 | | 50856 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.1 | 2.14 | | | 0.49 | 1.64 | 0.95 | | |
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 | 2.1 | 38.66 | 25669 | 1317 | 99.67 | 0.20624 | 0.2037 | 0.21 | 0.25783 | 0.26 | RANDOM | 37.965 |
| 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] |
|---|
| -0.64 | | | -0.07 | | 0.71 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 15.42 |
| r_dihedral_angle_2_deg | 14.232 |
| r_long_range_B_other | 11.283 |
| r_long_range_B_refined | 11.28 |
| r_scangle_other | 7.897 |
| r_dihedral_angle_1_deg | 6.899 |
| r_scbond_it | 5.046 |
| r_scbond_other | 5.044 |
| r_mcangle_other | 4.481 |
| r_mcangle_it | 4.48 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 15.42 |
| r_dihedral_angle_2_deg | 14.232 |
| r_long_range_B_other | 11.283 |
| r_long_range_B_refined | 11.28 |
| r_scangle_other | 7.897 |
| r_dihedral_angle_1_deg | 6.899 |
| r_scbond_it | 5.046 |
| r_scbond_other | 5.044 |
| r_mcangle_other | 4.481 |
| r_mcangle_it | 4.48 |
| r_mcbond_it | 3.041 |
| r_mcbond_other | 3.034 |
| r_angle_refined_deg | 1.45 |
| r_angle_other_deg | 0.506 |
| r_chiral_restr | 0.069 |
| r_bond_refined_d | 0.008 |
| r_gen_planes_refined | 0.007 |
| 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 | 2887 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 74 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| CrystFEL | data scaling |
| CrystFEL | data reduction |
| MOLREP | phasing |