X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 295.0
Details 1.5 M Li2SO4, 0.2 M MES pH 6.0, 0.02 M Magnesium sulfate, and 0.002 M spermine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.56 α = 90
b = 116.56 β = 90
c = 57.93 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Rh coated flat mirror, toroidal focusing mirror 2010-04-16
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 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
2.85 50 99.2 0.075 -- -- 7.2 -- 5771 0.0 -3.0 70.4
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)
2.85 2.95 100.0 0.357 -- -- 8.4 558

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
FOURIER SYNTHESIS 2.85 27.84 -- 0.0 -- 5639 561 97.58 -- 0.2306 0.226 0.2722 copied R-free set from 3GCA
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 2.85 3.1366 -- 129 1210 0.3714 0.3643 -- 95.0
X Ray Diffraction 3.1366 3.5897 -- 136 1243 0.2379 0.3131 -- 98.0
X Ray Diffraction 3.5897 4.5195 -- 143 1279 0.2294 0.2707 -- 99.0
X Ray Diffraction 4.5195 27.841 -- 153 1346 0.1907 0.2403 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.6848
Anisotropic B[1][1] 10.6047
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 10.6047
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -21.2094
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.056
f_angle_d 0.844
f_bond_d 0.006
f_plane_restr 0.008
f_dihedral_angle_d 19.382
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 680
Heterogen Atoms 6
Solvent Atoms 4

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement version: 1.6.4_486
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing version: 1.6.4_486