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
MOLECULAR REPLACEMENT 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_symmetry_vdw_refined 0.174
r_symmetry_hbond_refined 0.204
r_gen_planes_refined 0.01
r_symmetry_vdw_other 0.284
r_dihedral_angle_1_deg 5.138
r_chiral_restr 0.161
r_dihedral_angle_3_deg 16.761
r_angle_refined_deg 1.91
r_gen_planes_other 0.003
r_angle_other_deg 1.941
r_mcangle_it 2.871
r_symmetry_hbond_other 0.302
r_nbd_refined 0.262
r_nbtor_other 0.155
r_mcbond_it 1.935
r_bond_refined_d 0.02
r_nbd_other 0.218
r_xyhbond_nbd_other 0.009
r_scangle_it 4.683
r_xyhbond_nbd_refined 0.242
r_bond_other_d 0.001
r_scbond_it 3.276
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

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
CCP4 phasing