X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.4
Details PROTEIN AT 10MG/ML IN 15MM NACL, 10MM HEPES, PH7.4, MIXED WITH WELL BUFFER (50MM AMMONIUM ACETATE, 10% PEG4K, 0.1M HEPES PH 7.4) IN EQUAL VOLUMES, THEN VAPOUR DIFFUSION AGAINST WELL BUFFER. CDK2 CRYSTALS WERE SOAKED FOR 20 HOURS IN A SOLUTION OF 0.5MM NU2058 IN 1X WELL BUFFER PREPARED FROM STOCKS 2X WELLBUFFER AND 10MM NU2058 IN 100% DMSO.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.86 α = 90
b = 71.07 β = 90
c = 71.84 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
CCD MARRESEARCH TORROIDAL MIRROR 1998-04-25
Diffraction Radiation
Monochromator Protocol
DIAMOND SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 -- ESRF ID14-3

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
1.3 20 96.3 0.046 -- -- 2.3 -- 63538 -- 0.0 --
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)
1.3 1.36 97.2 0.471 -- 1.8 2.3 --

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
OTHER 1.3 50.64 -- -- -- 60158 3380 94.5 -- 0.153 0.151 0.185 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 1.3 1.33 -- 177 3293 0.279 0.314 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.44
Anisotropic B[1][1] -0.34
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.98
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.683
r_scbond_it 3.276
r_mcangle_it 2.871
r_mcbond_it 1.935
r_nbd_refined 0.262
r_gen_planes_other 0.003
r_gen_planes_refined 0.01
r_chiral_restr 0.161
r_dihedral_angle_3_deg 16.761
r_dihedral_angle_1_deg 5.138
r_angle_other_deg 1.941
r_angle_refined_deg 1.91
r_bond_other_d 0.001
r_bond_refined_d 0.02
r_nbd_other 0.218
r_nbtor_other 0.155
r_xyhbond_nbd_refined 0.242
r_xyhbond_nbd_other 0.009
r_symmetry_vdw_refined 0.174
r_symmetry_vdw_other 0.284
r_symmetry_hbond_refined 0.204
r_symmetry_hbond_other 0.302
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2342
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 345

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CCP4 Structure Solution
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CCP4 model building