X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch
pH 4.7
Temperature 295.0
Details HEWL co-crystallized with cisplatin with 5% DMSO media in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7, BATCH, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.04 α = 90
b = 79.04 β = 90
c = 38.04 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 295
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD APEX II CCD -- 2012-01-25
Diffraction Radiation
Monochromator Protocol
confocal mirror optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 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
2.4 55.89 53.3 0.18 -- -- 39.9 9038 4818 4.0 2.0 --
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)
2.4 2.44 100.0 0.947 -- 6.7 30.5 --

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 2.4 55.886 2.0 4.0 9038 4818 234 99.96 -- 0.16493 0.16258 0.2104 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 2.4 2.462 -- 19 289 0.169 0.334 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.873
Anisotropic B[1][1] -0.34
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.68
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.006
r_chiral_restr 0.101
r_dihedral_angle_4_deg 21.038
r_dihedral_angle_3_deg 16.515
r_dihedral_angle_2_deg 39.762
r_dihedral_angle_1_deg 7.243
r_angle_refined_deg 2.399
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 23

Software

Computing
Computing Package Purpose
APEX Data Collection
EVAL 15 Data Reduction (intensity integration)
EVAL 15 Data Reduction (data scaling)
Phaser MR Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
Phaser version: MR model building
APEX data collection