8GI3
Crystal structure of RhoA mutant L69P complexed with GDP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6V6U |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.1 | 293.2 | 0.2 M Ammonium citrate dibasic (pH 5.1), 20% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.048 | α = 90 |
b = 64.081 | β = 90 |
c = 82.504 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX300-HS | 2022-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.52 | 50.66 | 99.7 | 0.11 | 0.12 | 0.046 | 0.988 | 13.1 | 6.5 | 26852 | 11.25 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.52 | 1.55 | 99.7 | 0.143 | 0.154 | 0.058 | 0.98 | 10.6 | 6.6 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.52 | 50.66 | 26852 | 1341 | 99.54 | 0.1725 | 0.17057 | 0.20947 | RANDOM | 13.318 |
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 | -0.14 | 0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 16.401 |
r_dihedral_angle_2_deg | 7.712 |
r_dihedral_angle_1_deg | 5.913 |
r_long_range_B_refined | 5.782 |
r_long_range_B_other | 5.638 |
r_scangle_other | 4.11 |
r_scbond_other | 2.74 |
r_scbond_it | 2.737 |
r_mcangle_other | 2.473 |
r_mcangle_it | 2.472 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1417 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
SERGUI | data collection |
MOLREP | phasing |
REFMAC | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
Aimless | data scaling |