X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch
pH 4.7
Temperature 295.0
Details 49 mg HEWL + 3 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 4.7, BATCH, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.08 α = 90
b = 78.08 β = 90
c = 37.11 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 Bruker Platinum 135 Incoatec Helios confocal optics 2010-11-25
Diffraction Radiation
Monochromator Protocol
NONE 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
1.7 37.1 93.8 0.023 0.023 -- 24.27 13147 12342 4.0 2.0 14.7
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)
1.7 1.8 97.1 0.173 -- 4.02 16.21 13147

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 1.7 34.92 2.0 4.0 13147 12342 641 99.13 0.1852 0.18437 0.18156 0.23922 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 1.7 1.743 -- 46 847 0.19 0.288 -- 94.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.939
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.523
r_scbond_it 3.668
r_mcangle_it 1.9
r_mcbond_it 1.178
r_gen_planes_refined 0.01
r_chiral_restr 0.156
r_dihedral_angle_4_deg 18.804
r_dihedral_angle_3_deg 12.464
r_dihedral_angle_2_deg 36.663
r_dihedral_angle_1_deg 6.155
r_angle_refined_deg 1.911
r_bond_refined_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 98

Software

Computing
Computing Package Purpose
PROTEUM PLUS Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK 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
PROTEUM version: PLUS data collection