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_scangle_it 4.373
r_bond_refined_d 0.015
r_angle_refined_deg 1.498
r_dihedral_angle_1_deg 5.367
r_chiral_restr 0.106
r_gen_planes_refined 0.006
r_nbd_refined 0.204
r_xyhbond_nbd_refined 0.144
r_symmetry_vdw_refined 0.197
r_symmetry_hbond_refined 0.193
r_mcbond_it 0.785
r_mcangle_it 1.535
r_scbond_it 2.644
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6432
Nucleic Acid Atoms 0
Heterogen Atoms 102
Solvent Atoms 617

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement