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 = 96.49 β = 103.3
c = 67.64 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 -- 2009-10-17
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
1.95 24.61 98.6 -- -- -- -- -- 46922 2.0 2.0 25.71
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)
1.95 2.06 98.6 -- -- -- -- --

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 1.95 24.614 -- 1.42 -- 46888 1999 98.45 0.206 0.1893 0.1875 0.2304 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 1.95 1.9988 -- 140 3131 0.2429 0.3061 -- 96.0
X Ray Diffraction 1.9988 2.0528 -- 138 3119 0.2076 0.251 -- 97.0
X Ray Diffraction 2.0528 2.1131 -- 142 3164 0.1812 0.2537 -- 97.0
X Ray Diffraction 2.1131 2.1813 -- 141 3169 0.1813 0.2199 -- 97.0
X Ray Diffraction 2.1813 2.2592 -- 140 3166 0.1882 0.2639 -- 98.0
X Ray Diffraction 2.2592 2.3496 -- 142 3174 0.1948 0.2502 -- 98.0
X Ray Diffraction 2.3496 2.4564 -- 143 3204 0.1914 0.2474 -- 99.0
X Ray Diffraction 2.4564 2.5858 -- 144 3215 0.1951 0.267 -- 99.0
X Ray Diffraction 2.5858 2.7476 -- 142 3228 0.1946 0.2471 -- 99.0
X Ray Diffraction 2.7476 2.9595 -- 144 3222 0.1898 0.2436 -- 99.0
X Ray Diffraction 2.9595 3.2567 -- 145 3257 0.1867 0.2327 -- 100.0
X Ray Diffraction 3.2567 3.7265 -- 146 3256 0.1811 0.23 -- 100.0
X Ray Diffraction 3.7265 4.6897 -- 145 3270 0.1647 0.195 -- 100.0
X Ray Diffraction 4.6897 24.6163 -- 147 3314 0.1985 0.2059 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.7245
Anisotropic B[1][1] 1.4721
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.9941
Anisotropic B[2][2] 1.304
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.7761
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.079
f_dihedral_angle_d 13.942
f_angle_d 1.113
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4761
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 282

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