4RW3
Structural insights into substrate binding of brown spider venom class II phospholipases D
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RLH | PDB Entry 3RLH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 0.1 M Tris-HCl pH 7.5, 40% PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.97 | 37.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.81 | α = 90 |
b = 49.3 | β = 105.83 |
c = 56.3 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 200 | CCD | MARMOSAIC 225 mm CCD | 2014-03-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.458 | LNLS | W01B-MX2 |
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 | 1.72 | 30 | 28074 | 25218 |
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 | PDB Entry 3RLH | 1.72 | 30 | 25218 | 2808 | 99.83 | 0.18703 | 0.18295 | 0.223 | RANDOM | 19.529 |
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] | |
0.09 | 0.06 | 0.12 | -0.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.2 |
r_dihedral_angle_4_deg | 15.144 |
r_dihedral_angle_3_deg | 12.898 |
r_dihedral_angle_1_deg | 5.887 |
r_long_range_B_refined | 5.238 |
r_mcangle_it | 1.435 |
r_scbond_it | 1.385 |
r_angle_refined_deg | 1.343 |
r_mcbond_it | 0.899 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2197 |
Nucleic Acid Atoms | |
Solvent Atoms | 168 |
Heterogen Atoms | 149 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |