X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details Ammonium sulfate, tri-sodium citrate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.62 α = 90
b = 133.62 β = 90
c = 174.19 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Flat collimating mirror; double crystal Si(111) monochromator; toroid mirror (vertical and horizontal focusing) 2000-05-17
Diffraction Radiation
Monochromator Protocol
Flat collimating mirror; double crystal Si(111) monochromator; toroid mirror (vertical and horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1.03 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
2.1 40 96.6 0.084 0.084 -- 12.0 54042 52210 0.0 -3.0 18.8
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)
2.1 2.16 92.0 0.263 0.263 6.64 6.0 --

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
Difference Fourier 2.1 43.83 -3.0 0.0 54042 52210 5254 96.6 0.197 0.197 0.197 0.222 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 2.1 2.23 -- 800 7359 0.225 0.248 0.009 92.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.7
Anisotropic B[1][1] 3.75
Anisotropic B[1][2] 3.71
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.5
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 1.76
c_bond_d 0.005
c_scbond_it 1.83
c_mcbond_it 1.16
c_scangle_it 2.59
c_dihedral_angle_d 22.9
c_improper_angle_d 0.83
c_angle_deg 1.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3864
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 270

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
CNS phasing