X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 289.0
Details 8.5% PEG 6000, 0.1M MES, 1mM DTT, 1mM EDTA, 3% DMSO, 10% Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.32 α = 90
b = 97.1 β = 103.17
c = 67.4 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2009-09-18
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
2.2 34.1 100.0 -- -- -- -- -- 33359 2.0 2.0 33.25
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)
2.2 2.32 100.0 -- -- -- -- --

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 2.2 32.816 -- 1.43 -- 33309 1997 99.92 0.2 0.1849 0.1817 0.2354 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 2.2 2.255 -- 141 2232 0.2435 0.3138 -- 100.0
X Ray Diffraction 2.255 2.316 -- 142 2219 0.2191 0.282 -- 100.0
X Ray Diffraction 2.316 2.3841 -- 141 2212 0.2208 0.3016 -- 100.0
X Ray Diffraction 2.3841 2.461 -- 144 2246 0.2003 0.2519 -- 100.0
X Ray Diffraction 2.461 2.5489 -- 141 2216 0.19 0.2534 -- 100.0
X Ray Diffraction 2.5489 2.651 -- 142 2218 0.1851 0.2658 -- 100.0
X Ray Diffraction 2.651 2.7715 -- 145 2266 0.1766 0.2564 -- 100.0
X Ray Diffraction 2.7715 2.9176 -- 142 2229 0.1713 0.2308 -- 100.0
X Ray Diffraction 2.9176 3.1003 -- 142 2224 0.165 0.2334 -- 100.0
X Ray Diffraction 3.1003 3.3394 -- 142 2235 0.1629 0.2138 -- 100.0
X Ray Diffraction 3.3394 3.6751 -- 143 2242 0.1562 0.2084 -- 100.0
X Ray Diffraction 3.6751 4.2059 -- 144 2253 0.1719 0.22 -- 100.0
X Ray Diffraction 4.2059 5.2954 -- 144 2253 0.166 0.2169 -- 100.0
X Ray Diffraction 5.2954 32.8198 -- 144 2267 0.2201 0.2407 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.8982
Anisotropic B[1][1] -0.6346
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.8616
Anisotropic B[2][2] 6.4174
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.7828
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.069
f_dihedral_angle_d 14.344
f_angle_d 1.077
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4775
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 201

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHASES model building
CrystalClear data collection