4GCD
Room temperature X-ray diffraction study of a 6-fold molar excess of a cisplatin/carboplatin mixture binding to HEWL, Dataset 2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2W1Y | PDB ENTRY 2W1Y |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.7 | 277 | 49 mg HEWL (3.2 mM), 3 mg cisplatin (10 mM), 3.7 mg carboplatin (10 mM) in 0.04 M sodium acetate buffer (462.5 uL) + 10% sodium chloride precipitant (462.5 uL) + 1 mM DMSO (75 uL), pH 4.7, BATCH, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.863 | α = 90 |
b = 79.863 | β = 90 |
c = 37.802 | 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 | 300 | CCD | APEX II CCD | 2012-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR-H | 1.5418 |
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 | 2.8 | 35.74 | 100 | 0.289 | 10.8 | 23.6 | 3140 | 3141 | 4 | 2 |
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 | 2.8 | 2.87 | 100 | 0.575 | 4.5 | 25.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | 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 2W1Y | 2.8 | 35.74 | 2 | 4 | 3140 | 3141 | 152 | 99.85 | 0.17845 | 0.17535 | 0.24007 | RANDOM | 34.654 |
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] | |
-0.19 | -0.19 | 0.38 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.475 |
r_dihedral_angle_4_deg | 22.312 |
r_dihedral_angle_3_deg | 17.737 |
r_dihedral_angle_1_deg | 6.996 |
r_angle_refined_deg | 1.585 |
r_angle_other_deg | 0.846 |
r_chiral_restr | 0.079 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 6 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
APEX | data collection |
PHASER | phasing |
REFMAC | refinement |
APEX | data reduction |