X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 7.8
Temperature 291.0
Details 0.1 M Imidazole pH 7.8, 20 %(w/v) PEG 6000, 15 mg/ml PKM2, EVAPORATION, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 168.12 α = 90
b = 94.14 β = 99.39
c = 146.15 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B -- APS 14-ID-B

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
2.3 50 99.7 0.125 0.125 -- 5.1 94346 94063 -- 1.0 --

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 2.3 40.24 1.0 0.0 -- 94063 4951 99.01 0.2142 -- 0.2115 0.2662 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 2.3 2.36 -- 399 6859 0.279 0.349 -- 98.59
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.2193
Anisotropic B[1][1] -0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.02
Anisotropic B[2][2] 0.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.08
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_chiral_restr 0.085
r_dihedral_angle_4_deg 18.515
r_dihedral_angle_3_deg 16.24
r_dihedral_angle_2_deg 37.016
r_dihedral_angle_1_deg 5.528
r_angle_refined_deg 1.293
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15860
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 222

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASES Structure Solution
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.7.0029 refinement