2HEI
Crystal structure of human RAB5B in complex with GDP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1N6I | PDB ENTRY 1N6I |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 291 | 25% P3350, 0.1M NaOAc, pH 4.5, vapor diffusion, sitting drop, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 37.04 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 41.302 | ¦Á = 90 |
b = 78.37 | ¦Â = 90 |
c = 95.501 | ¦Ã = 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 | ADSC QUANTUM 4 | 2006-05-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE F1 | CHESS | F1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.5 | 50 | 100 | 0.058 | 9.2 | 7 | 50161 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.5 | 1.55 | 100 | 0.679 | 6.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1N6I | 1.55 | 30 | 45443 | 2875 | 99.184 | 0.264 | 0.2622 | 0.2936 | thin shells | 15.121 |
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] | |
-0.375 | 0.517 | -0.143 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.633 |
r_dihedral_angle_4_deg | 14.429 |
r_dihedral_angle_3_deg | 12.151 |
r_dihedral_angle_1_deg | 6.085 |
r_scangle_it | 3.232 |
r_mcangle_it | 2.907 |
r_scbond_it | 2.466 |
r_mcbond_it | 2.432 |
r_angle_refined_deg | 1.488 |
r_angle_other_deg | 1.139 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2568 |
Nucleic Acid Atoms | |
Solvent Atoms | 124 |
Heterogen Atoms | 72 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ARP/wARP | model building |
MolProbity | model building |