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 -- 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_scangle_it 3.258
r_scbond_it 2.232
r_mcangle_it 1.411
r_mcbond_it 0.874
r_nbd_refined 0.239
r_gen_planes_refined 0.007
r_chiral_restr 0.122
r_dihedral_angle_4_deg 18.457
r_dihedral_angle_3_deg 18.051
r_dihedral_angle_2_deg 39.556
r_dihedral_angle_1_deg 6.585
r_angle_refined_deg 1.69
r_bond_refined_d 0.018
r_nbtor_refined 0.314
r_xyhbond_nbd_refined 0.22
r_symmetry_vdw_refined 0.282
r_symmetry_hbond_refined 0.247
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0003 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0003 refinement
MOLREP model building