X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details PCDK2/CYCLIN E (6-8 MG/ML), 1 MM AMPPNP, 10-15% PEG3350, 0.2 M SODIUM CITRATE PH7.5, pH 7.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.62 α = 90
b = 99.62 β = 90
c = 149.99 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- 2004-08-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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
2.13 34.28 94.2 0.08 -- -- 4.0 -- 39329 -- 1.5 --
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)
2.13 2.21 53.8 0.48 -- 1.9 3.5 --

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 2.15 83.05 -- -- -- 37310 1984 94.2 -- 0.185 0.181 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 2.15 2.21 -- 80 1221 0.216 0.339 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.24
Anisotropic B[1][1] 0.72
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.44
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.874
r_symmetry_vdw_refined 0.282
r_dihedral_angle_4_deg 18.457
r_symmetry_hbond_refined 0.247
r_gen_planes_refined 0.007
r_scangle_it 3.258
r_bond_refined_d 0.018
r_chiral_restr 0.122
r_angle_refined_deg 1.69
r_xyhbond_nbd_refined 0.22
r_scbond_it 2.232
r_nbtor_refined 0.314
r_mcangle_it 1.411
r_dihedral_angle_3_deg 18.051
r_dihedral_angle_1_deg 6.585
r_dihedral_angle_2_deg 39.556
r_nbd_refined 0.239
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4617
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 547

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0003
MOSFLM data reduction
SCALA data scaling
MOLREP phasing