X-RAY DIFFRACTION Experimental Data & Validation


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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 = 52.1 α = 90
b = 96.43 β = 103.48
c = 67.69 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 -- 2009-10-14
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
2.5 29.61 99.9 -- -- -- -- -- 22586 2.0 2.0 34.48
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)
2.5 2.64 100.0 -- -- -- -- --

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 2.5 28.986 -- 1.49 -- 22556 1999 99.94 0.212 0.1933 0.1881 0.2453 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 2.5001 2.5626 -- 141 1443 0.2172 0.3077 -- 100.0
X Ray Diffraction 2.5626 2.6318 -- 142 1462 0.2324 0.3094 -- 100.0
X Ray Diffraction 2.6318 2.7092 -- 142 1470 0.2431 0.2938 -- 100.0
X Ray Diffraction 2.7092 2.7966 -- 141 1454 0.2219 0.3298 -- 100.0
X Ray Diffraction 2.7966 2.8964 -- 144 1481 0.2113 0.3209 -- 100.0
X Ray Diffraction 2.8964 3.0123 -- 141 1443 0.1788 0.2401 -- 100.0
X Ray Diffraction 3.0123 3.1492 -- 144 1473 0.178 0.2445 -- 100.0
X Ray Diffraction 3.1492 3.315 -- 142 1458 0.1925 0.2719 -- 100.0
X Ray Diffraction 3.315 3.5224 -- 142 1473 0.1873 0.2498 -- 100.0
X Ray Diffraction 3.5224 3.7938 -- 144 1475 0.1957 0.2429 -- 100.0
X Ray Diffraction 3.7938 4.1746 -- 142 1465 0.169 0.2101 -- 100.0
X Ray Diffraction 4.1746 4.7763 -- 145 1482 0.1504 0.2242 -- 100.0
X Ray Diffraction 4.7763 6.0089 -- 143 1473 0.1874 0.2164 -- 100.0
X Ray Diffraction 6.0089 28.9875 -- 146 1505 0.1933 0.2102 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.4448
Anisotropic B[1][1] 3.6669
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 7.5477
Anisotropic B[2][2] 5.4377
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -9.1046
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.072
f_dihedral_angle_d 14.232
f_angle_d 1.129
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4761
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 134

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