2VRP
Structure of rhodocytin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IOD | COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR |
experimental model | PDB | 1J34 | COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR |
experimental model | PDB | 1C3A | COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR |
experimental model | PDB | 1UMR | COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8 | 2M AMMONIUM SULPHATE, 5% 2-PROPANOL, pH 8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.933 | α = 90 |
b = 89.368 | β = 90 |
c = 120.996 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | MARRESEARCH | MIRRORS | 2007-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.4 | 50 | 94.7 | 0.04 | 37.75 | 4 | 13367 | -3 |
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 | 2.4 | 2.49 | 80.8 | 0.12 | 7.05 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR | 2.41 | 36.76 | 12040 | 618 | 94.4 | 0.204 | 0.201 | 0.272 | RANDOM | 38.94 |
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] | |
0.1 | 0.56 | -0.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.547 |
r_dihedral_angle_3_deg | 22.436 |
r_dihedral_angle_4_deg | 20.569 |
r_dihedral_angle_1_deg | 8.822 |
r_scangle_it | 3.438 |
r_scbond_it | 2.161 |
r_angle_refined_deg | 1.916 |
r_mcangle_it | 1.704 |
r_mcbond_it | 0.872 |
r_nbtor_refined | 0.311 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2101 |
Nucleic Acid Atoms | |
Solvent Atoms | 44 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
BALBES | phasing |