X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 300.0
Details 0.4-0.6 M sodium citrate, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 300.0
Details 12% polyethylene 3350, 0.2 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 267.2 α = 90
b = 267.2 β = 90
c = 149.5 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2006-10-20
Diffraction Radiation
Monochromator Protocol
-- MAD
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0,1.2199,1.2815,1.2826,1.2830 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
3.29 35 98.9 0.095 -- -- 5.8 -- 47346 -- -3.0 --
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)
3.29 3.41 99.1 0.489 -- 3.9 -- --

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
MAD 3.3 29.74 -- 0.0 -- 46954 2344 98.8 -- 0.248 0.248 0.272 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 3.3 3.42 -- 220 4404 0.375 0.403 0.027 99.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 114.0
Anisotropic B[1][1] 2.13
Anisotropic B[1][2] 15.28
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.26
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 8.83
c_dihedral_angle_d 23.7
c_improper_angle_d 0.96
c_mcbond_it 6.33
c_bond_d 0.008
c_scangle_it 12.74
c_mcangle_it 10.36
c_angle_deg 1.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.47
Luzzati Sigma A (Observed) 0.42
Luzzati Resolution Cutoff (Low) 40.0
Luzzati ESD (R-Free Set) 0.53
Luzzati Sigma A (R-Free Set) 0.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7852
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 0

Software

Software
Software Name Purpose
MAR345dtb data collection
SnB phasing
CNS refinement version: 1.1
HKL-2000 data reduction
HKL-2000 data scaling