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
2.9 56.47 99.8 0.38 -- -- 23.2 2820 2816 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)
2.9 2.97 100.0 0.627 -- 3.5 25.7 --

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 2.9 56.47 2.0 4.0 2820 2816 138 99.76 -- 0.17673 0.17378 0.23407 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 2.9 2.975 -- 5 160 0.31 0.531 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.617
Anisotropic B[1][1] -0.8
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.8
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.61
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.071
r_dihedral_angle_4_deg 18.313
r_dihedral_angle_3_deg 14.764
r_dihedral_angle_2_deg 42.162
r_dihedral_angle_1_deg 6.144
r_angle_other_deg 0.874
r_angle_refined_deg 1.311
r_bond_other_d 0.001
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 5

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