X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 293.0
Details 10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.19 α = 90
b = 72.43 β = 90
c = 71.94 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2018-02-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04

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
1.06 72.43 84.9 0.11 -- -- 5.6 -- 107335 -- -- --
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)
1.06 1.08 5.6 0.5 -- 0.7 1.1 --

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 1.06 51.09 -- -- -- 102042 5293 84.92 -- 0.18034 0.17901 0.20514 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 1.06 1.087 -- 33 847 0.356 0.442 -- 9.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.395
Anisotropic B[1][1] 1.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.5
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.963
r_mcangle_it 3.325
r_gen_planes_other 0.021
r_dihedral_angle_2_deg 37.847
r_gen_planes_refined 0.014
r_chiral_restr 0.116
r_scbond_other 3.406
r_angle_other_deg 2.325
r_long_range_B_other 4.706
r_scangle_other 4.328
r_bond_other_d 0.033
r_mcangle_other 3.324
r_bond_refined_d 0.015
r_mcbond_it 3.047
r_dihedral_angle_4_deg 17.603
r_scbond_it 3.405
r_rigid_bond_restr 20.022
r_long_range_B_refined 4.707
r_mcbond_other 3.046
r_angle_refined_deg 1.997
r_dihedral_angle_3_deg 15.095
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2290
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 300

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0238
xia2 data reduction
Aimless data scaling
PHASER phasing