X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 298.0
Details PEG600, cacodylate, acetylCoA, pH 6.5, VAPOR DIFFUSION, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.88 α = 90
b = 146.88 β = 90
c = 129.51 γ = 120
Symmetry
Space Group P 62

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-09-08
Diffraction Radiation
Monochromator Protocol
Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9330 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 20 99.0 -- 0.078 -- 6.5 105732 105732 2.0 2.0 --
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)
2.0 2.11 97.5 -- 0.265 -- -- --

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 2.0 20.0 -- 2.0 105732 96936 8795 99.08 0.1592 0.1592 0.15769 0.17598 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 2.0 2.051 -- 631 6865 0.19 0.21 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.857
Anisotropic B[1][1] -1.38
Anisotropic B[1][2] -0.69
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.07
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.204
r_mcangle_it 1.535
r_dihedral_angle_1_deg 5.367
r_mcbond_it 0.785
r_scbond_it 2.644
r_angle_refined_deg 1.498
r_symmetry_hbond_refined 0.193
r_chiral_restr 0.106
r_symmetry_vdw_refined 0.197
r_xyhbond_nbd_refined 0.144
r_scangle_it 4.373
r_bond_refined_d 0.015
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6432
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 617

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
DENZO data reduction
CCP4 data scaling version: (SCALA)
AMoRE phasing