X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details D-SEDOHEPTULOSE-7-PHOSPHATE, AMMONIUM SULPHATE, K/NA TARTRATE, NA CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.34 α = 90
b = 126.34 β = 90
c = 113.24 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 MIRRORS 2004-08-06
Diffraction Radiation
Monochromator Protocol
SI(111)DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.07229 APS 17-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
2.3 40 99.9 0.125 -- -- 12.4 24669 24669 0.0 -3.0 21.3
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)
2.3 2.38 100.0 0.404 -- 6.17 12.6 --

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 39.34 -- 0.0 24221 24221 1222 99.9 -- 0.176 0.176 0.221 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 2.44 -- 190 3752 0.192 0.278 0.02 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.1
Anisotropic B[1][1] -4.75
Anisotropic B[1][2] 1.56
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.5
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.08
c_angle_deg 1.8
c_bond_d 0.019
c_mcbond_it 1.31
c_improper_angle_d 1.21
c_mcangle_it 1.97
c_scbond_it 2.75
c_dihedral_angle_d 21.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2968
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 196

Software

Software
Software Name Purpose
CNS refinement version: 1.1
HKL-2000 data reduction
SCALEPACK data scaling
CNS phasing