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_improper_angle_d 1.77
c_dihedral_angle_d 14.0
c_angle_deg 1.2
c_bond_d 0.007
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 2048
Heterogen Atoms 10
Solvent Atoms 416

Software

Computing
Computing Package Purpose
MAR, DENZO Data Reduction (intensity integration)
XDISP, SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
CNS model building
XDISP/DENZO data reduction
MAR data collection