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,oxalate, acethylCoA , pH 6.5, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.79 α = 90
b = 146.79 β = 90
c = 129.9 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 210 mirrors 2003-04-09
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.979257 ESRF ID29

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
2.2 20 98.7 -- 0.114 -- 4.0 79388 79388 -- 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)
2.2 2.32 98.3 -- 0.234 3.0 4.0 --

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 2.2 20.0 -- 0.0 79388 72739 6647 98.8 0.1825 0.18251 0.18056 0.2037 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 2.2 2.256 -- 465 5284 0.224 0.257 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.451
Anisotropic B[1][1] -1.65
Anisotropic B[1][2] -0.83
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.48
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.213
r_gen_planes_refined 0.007
r_chiral_restr 0.101
r_dihedral_angle_1_deg 6.032
r_angle_refined_deg 1.623
r_bond_refined_d 0.017
r_xyhbond_nbd_refined 0.191
r_symmetry_vdw_refined 0.179
r_symmetry_hbond_refined 0.186
r_mcbond_it 0.848
r_mcangle_it 1.559
r_scbond_it 2.669
r_scangle_it 4.162
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6440
Nucleic Acid Atoms 0
Heterogen Atoms 144
Solvent Atoms 454

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