X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch
pH 6.5
Temperature 277.0
Details 20 mg HEWL + 1.1 mg cisplatin in 462.5 uL 0.04 M sodium acetate + 75 uL DMSO + 462.5 uL 10% sodium chloride, with paratone as cryoprotectant, pH 6.5, BATCH, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.46 α = 90
b = 79.46 β = 90
c = 36.96 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU RAXIS IV Osmic Confocal Max-Flux, blue configuration 2011-05-09
Diffraction Radiation
Monochromator Protocol
NONE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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
3 56.19 56.9 0.15 0.15 -- 3.18 4150 2365 4.0 2.0 27.9
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.0 3.11 91.3 0.226 -- 3.2 3.15 4150

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 3.0 33.51 2.0 4.0 4150 2365 109 94.54 -- 0.2136 0.21141 0.25852 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.0 3.077 -- 11 174 0.321 0.224 -- 96.35
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.113
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.181
r_scbond_it 1.301
r_mcangle_it 0.795
r_mcbond_it 0.405
r_gen_planes_refined 0.005
r_chiral_restr 0.103
r_dihedral_angle_4_deg 21.234
r_dihedral_angle_3_deg 20.305
r_dihedral_angle_2_deg 41.853
r_dihedral_angle_1_deg 7.208
r_angle_refined_deg 1.691
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 7

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHASER MOLECULAR REPLACEMENT Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0110 refinement
PHASER version: MOLECULAR REPLACEMENT model building
CrystalClear data collection