4BXS
Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KIG | UNPUBLISHED FV STRUCTURE AND PDB ENTRY 1KIG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 0.1 M MORPHEUS BUFFER 3, 20% MORPHEUS P20K_P550MME, 50 MM MORPHEUS CARBOXYLIC ACIDS, pH 8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.72 | 66.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 115.31 | α = 90 |
b = 115.31 | β = 90 |
c = 429.52 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | ADSC CCD | 2012-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 3.32 | 101.59 | 99.4 | 0.15 | 7.8 | 6 | 43913 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 3.32 | 3.5 | 95.1 | 1 | 1.5 | 5.4 |
Refinement
Statistics | |||||||||||||||||||
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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 | UNPUBLISHED FV STRUCTURE AND PDB ENTRY 1KIG | 3.32 | 89.81 | 41486 | 2241 | 99.1 | 0.30124 | 0.29773 | 0.36793 | RANDOM | 117.583 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
6.17 | 6.17 | -12.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.056 |
r_dihedral_angle_3_deg | 15.819 |
r_dihedral_angle_4_deg | 15.057 |
r_dihedral_angle_1_deg | 3.872 |
r_angle_refined_deg | 0.614 |
r_chiral_restr | 0.042 |
r_bond_refined_d | 0.002 |
r_gen_planes_refined | 0.002 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10995 |
Nucleic Acid Atoms | |
Solvent Atoms | 112 |
Heterogen Atoms | 188 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |