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 and NAG in 7.5% 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 = 78.82 α = 90
b = 78.82 β = 90
c = 38.02 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 -- 2012-01-24
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
2.1 55.74 52.6 0.177 -- -- 19.2 13385 7055 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)
2.1 2.13 100.0 0.749 -- 5.1 13.2 --

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 2.1 55.736 2.0 4.0 13385 7050 343 99.99 -- 0.16233 0.15927 0.22701 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 2.1 2.155 -- 18 432 0.159 0.219 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.044
Anisotropic B[1][1] -0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.2
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 39.27
r_bond_refined_d 0.018
r_gen_planes_other 0.001
r_angle_refined_deg 2.531
r_angle_other_deg 1.07
r_bond_other_d 0.001
r_dihedral_angle_4_deg 25.586
r_gen_planes_refined 0.008
r_dihedral_angle_1_deg 7.096
r_chiral_restr 0.118
r_dihedral_angle_3_deg 15.313
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 35

Software

Software
Software Name Purpose
APEX data collection
PHASER phasing version: MR
REFMAC refinement version: 5.6.0117
EVAL data reduction version: 15
EVAL data scaling version: 15