X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 50 mM Ammonium sulfate, 24-30% PEG 2000, 50 mM HEPES pH 8.0, 5% 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.42 α = 90
b = 62.42 β = 90
c = 58.89 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2006-08-22
Diffraction Radiation
Monochromator Protocol
Si(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-ID

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 50 90.7 0.133 0.133 -- 7.5 8117 8117 0.0 0.0 7.7
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 2.07 53.9 0.415 0.415 1.7 2.5 877

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 39.82 -- -- 8117 7699 829 86.6 0.228 0.211 0.211 0.265 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 2.07 429 47 738 0.272 0.285 0.03 53.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.2
Anisotropic B[1][1] 0.73
Anisotropic B[1][2] 1.98
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.73
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.46
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.82
c_scbond_it 2.47
c_mcangle_it 3.35
c_mcbond_it 1.97
c_improper_angle_d 0.68
c_dihedral_angle_d 25.7
c_angle_deg 1.1
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 748
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 82

Software

Computing
Computing Package Purpose
SER-CAT Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
CNS model building
SER-CAT data collection