X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.3
Temperature 291.0
Details PEGMME 2000, lithium sulphate, MPD, magnesium sulphate, ADP, pH 7.3, VAPOR DIFFUSION, temperature 291.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.62 α = 90
b = 110.62 β = 90
c = 335.83 γ = 120
Symmetry
Space Group P 6 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 double crystal monochromator, mirrors 2000-03-03
Diffraction Radiation
Monochromator Protocol
Double-Crystal Si 111 crystals SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1.0000 SSRL BL9-2

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 35.4 96.5 0.058 5.8 -- 3.17 53223 53223 0.0 0.0 11.5
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 2.34 95.3 0.124 12.4 8.5 2.7 2563

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 35.4 0.0 0.0 53223 49568 4983 89.9 0.264 0.264 0.264 0.276 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 6707 743 -- 0.387 0.394 0.014 83.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model group
Mean Isotropic B 46.2
Anisotropic B[1][1] -22.42
Anisotropic B[1][2] -0.56
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -22.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 44.84
RMS Deviations
Key Refinement Restraint Deviation
x_mcbond_it 7.1
x_scangle_it 15.8
x_scbond_it 11.1
x_dihedral_angle_d 21.2
x_improper_angle_d 1.14
x_mcangle_it 11.0
x_angle_deg 1.2
x_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.5
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.39
Luzzati Sigma A (R-Free Set) 0.47
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2567
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 97

Software

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing