5BWI
Crystallographic structure of a bacterial heparanase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3VNZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.8 M potassium sodium tartrate tetrahydrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.32 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 125.03 | ¦Á = 90 |
b = 125.03 | ¦Â = 90 |
c = 125.16 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 41 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 QUANTUM 210r | 2012-10-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.954 | Australian Synchrotron | MX1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.6 | 31.29 | 99.4 | 6.9 | 14.54 | 129599 |
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 | 3VNZ | 1.6 | 31.29 | 122996 | 6514 | 99.37 | 0.16563 | 0.16426 | 0.19187 | RANDOM | 19.61 |
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] | |
-0.06 | -0.06 | 0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.18 |
r_dihedral_angle_4_deg | 17.915 |
r_dihedral_angle_3_deg | 12.118 |
r_long_range_B_refined | 5.996 |
r_long_range_B_other | 5.996 |
r_dihedral_angle_1_deg | 5.99 |
r_scangle_other | 2.37 |
r_mcangle_it | 2.02 |
r_mcangle_other | 2.02 |
r_scbond_it | 1.469 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6319 |
Nucleic Acid Atoms | |
Solvent Atoms | 1223 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |