X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Temperature 291.0
Details 5 mg/mL CDK2 protein, 3 mM inhibitor, 15% v/v PEG3350, 50 mM HEPES/NaOH, 50 mM Na/K phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.66 α = 90
b = 71.73 β = 90
c = 72.57 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SATURN 944+ RIGAKU MIRRORS 2009-02-03
Diffraction Radiation
Monochromator Protocol
MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF -- -- --

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
1.95 20 99.8 0.067 -- -- 6.86 -- 20992 -- -3.0 12.3
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)
1.95 2.0 100.0 0.293 -- 6.71 6.83 --

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 1.95 18.79 -- 0.0 20992 20992 1155 99.7 -- 0.2 0.2 0.246 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 1.95 2.07 -- 189 3245 0.228 0.307 0.022 99.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 31.9
Anisotropic B[1][1] -4.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.4
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.05
c_scbond_it 2.1
c_mcangle_it 2.62
c_mcbond_it 1.61
c_improper_angle_d 0.87
c_bond_d 0.007
c_angle_deg 1.3
c_dihedral_angle_d 22.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2366
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 175

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
CNS 1.2 Structure Solution
CNS 1.2 Structure Refinement
Software
Software Name Purpose
CNS version: 1.2 refinement
CNS version: 1.2 model building
StructureStudio data collection