X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 291.0
Details 50mM Imidazole, 350mM sodium acetate, 17% Peg3350, pH 7.5, VAPOR DIFFUSION, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.86 α = 90
b = 78.79 β = 112.65
c = 55.15 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
CCD RIGAKU SATURN 92 mirrors 2011-05-17
Diffraction Radiation
Monochromator Protocol
mirrors Varimax HF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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 50 99.9 0.067 0.067 -- 4.8 -- n/a 0.0 -3.0 31.97
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)
2.0 2.07 100.0 0.411 -- 2.39 2.9 2927

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 1.998 22.888 -- 0.0 27692 27692 1369 94.08 0.2222 0.2222 0.2194 0.2779 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 1.9979 2.0693 -- 126 2504 0.2362 0.313 -- 90.0
X Ray Diffraction 2.0693 2.1521 -- 141 2636 0.2301 0.2929 -- 96.0
X Ray Diffraction 2.1521 2.2499 -- 143 2655 0.2257 0.3054 -- 95.0
X Ray Diffraction 2.2499 2.3685 -- 138 2570 0.2409 0.3149 -- 92.0
X Ray Diffraction 2.3685 2.5167 -- 123 2530 0.2492 0.354 -- 90.0
X Ray Diffraction 2.5167 2.7107 -- 131 2524 0.2542 0.324 -- 91.0
X Ray Diffraction 2.7107 2.983 -- 134 2536 0.2516 0.3187 -- 91.0
X Ray Diffraction 2.983 3.4134 -- 143 2746 0.2234 0.2601 -- 97.0
X Ray Diffraction 3.4134 4.2959 -- 147 2793 0.1885 0.2927 -- 99.0
X Ray Diffraction 4.2959 22.889 -- 143 2829 0.2087 0.216 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.9025
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.4272
Anisotropic B[2][2] 1.0471
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.9496
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.07
f_dihedral_angle_d 21.962
f_angle_d 1.192
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2522
Nucleic Acid Atoms 632
Heterogen Atoms 39
Solvent Atoms 188

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
CNS model building
StructureStudio data collection