X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 20.0
Details MPD, Mg-Acetate, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.1 α = 90
b = 60.1 β = 90
c = 133.1 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate 16 pole wiggler, Flat mirror, Si(311) bent mono with horizontal focus 1999-03-04
Diffraction Radiation
Monochromator Protocol
si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.98 SSRL BL9-1

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
1.8 34 95.2 -- 0.04 -- 3.1 -- 25779 -- -3.0 26.8
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)
1.8 1.83 87.4 -- 0.272 4.6 2.1 --

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
EXPAND TO P6(1) 1.8 29.31 -- 0.0 25173 23965 2142 95.2 -- 0.203 0.203 0.224 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 1.8 1.86 -- 196 1997 0.285 0.327 0.034 87.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.2
Anisotropic B[1][1] 4.43
Anisotropic B[1][2] -0.87
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.86
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_improper_angle_d 1.77
c_angle_deg 1.2
c_dihedral_angle_d 14.0
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.38
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 2072
Heterogen Atoms 10
Solvent Atoms 416

Software

Software
Software Name Purpose
MAR data collection
XDISP/DENZO data reduction
CNS refinement
MAR data reduction
DENZO data reduction
XDISP data scaling
SCALEPACK data scaling
CNS phasing