X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 298.0
Details 50 MM TRIS HCL, 15% PEG3350, 100MM CALCIUM DIACETATE, 2.5% GLYCEROL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.58 α = 90
b = 103.31 β = 90
c = 52.78 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2009-10-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 1.0 APS 21-ID-F

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
2.74 50 -- 0.088 -- -- -- -- 14000 -- 0.0 --
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)
2.75 2.85 -- 0.644 -- -- -- --

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
MOLECULAR REPLACEMENT 2.74 42.09 -- 1.34 -- 14000 1401 99.0 -- 0.209 0.203 0.265 --
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 2.7424 2.8404 -- 126 1139 0.4036 0.4511 -- 91.0
X Ray Diffraction 2.8404 2.9541 -- 139 1245 0.3252 0.4116 -- 99.0
X Ray Diffraction 2.9541 3.0885 -- 138 1239 0.2709 0.3328 -- 100.0
X Ray Diffraction 3.0885 3.2513 -- 139 1258 0.2213 0.2966 -- 100.0
X Ray Diffraction 3.2513 3.4549 -- 138 1236 0.2069 0.2929 -- 100.0
X Ray Diffraction 3.4549 3.7216 -- 141 1273 0.1977 0.248 -- 100.0
X Ray Diffraction 3.7216 4.0958 -- 141 1265 0.1926 0.2587 -- 100.0
X Ray Diffraction 4.0958 4.6878 -- 142 1276 0.1488 0.2097 -- 100.0
X Ray Diffraction 4.6878 5.9035 -- 145 1304 0.1836 0.2541 -- 100.0
X Ray Diffraction 5.9035 42.0951 -- 152 1364 0.1954 0.2298 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.1056
Anisotropic B[1][1] 5.6627
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.1584
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.5043
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.3
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2744
Nucleic Acid Atoms 576
Heterogen Atoms 32
Solvent Atoms 40

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
PHENIX (PHENIX.REFINE: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement