X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.7
Temperature 277.0
Details 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 Data

Unit Cell
Length (Å) Angle (°)
a = 79.86 α = 90
b = 79.86 β = 90
c = 37.8 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 300
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD APEX II CCD -- 2012-05-25
Diffraction Radiation
Monochromator Protocol
confocal mirror optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR-H 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 56.47 99.9 0.202 -- -- 9.8 8276 8270 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)
2.0 2.05 100.0 0.796 -- 1.42 6.9 --

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 2.0 56.47 2.0 4.0 8276 8270 415 99.97 -- 0.18885 0.18601 0.24842 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 2.0 2.052 -- 23 520 0.288 0.322 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.22
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] -0.69
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.112
r_dihedral_angle_4_deg 20.656
r_dihedral_angle_3_deg 15.769
r_dihedral_angle_2_deg 37.918
r_dihedral_angle_1_deg 6.805
r_angle_other_deg 1.036
r_angle_refined_deg 1.85
r_bond_other_d 0.003
r_bond_refined_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 44

Software

Computing
Computing Package Purpose
APEX Data Collection
APEX Data Reduction (intensity integration)
APEX 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