X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 0.2M MgCl2, 0.1M Tris-HCl, 30% (w/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.85 α = 90
b = 72.56 β = 90
c = 74.33 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2012-12-05
Diffraction Radiation
Monochromator Protocol
Varimax optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.85 20 95.7 -- -- -- -- 19938 19081 2.0 2.0 26.41
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)
1.92 1.99 94.0 -- -- -- -- --

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 1.851 19.407 -- 1.36 -- 19046 943 95.73 -- 0.1883 0.1861 0.2287 --
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 1.8515 1.949 -- 125 2458 0.2051 0.2904 -- 93.0
X Ray Diffraction 1.949 2.071 -- 129 2514 0.214 0.2684 -- 94.0
X Ray Diffraction 2.071 2.2307 -- 132 2499 0.1971 0.2474 -- 94.0
X Ray Diffraction 2.2307 2.4548 -- 129 2530 0.2044 0.2498 -- 95.0
X Ray Diffraction 2.4548 2.8091 -- 141 2625 0.2105 0.2496 -- 97.0
X Ray Diffraction 2.8091 3.5356 -- 136 2655 0.1911 0.2449 -- 98.0
X Ray Diffraction 3.5356 19.4081 -- 151 2822 0.1591 0.1882 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.98
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_bond_d 0.011
f_dihedral_angle_d 18.576
f_angle_d 1.4
f_chiral_restr 0.082
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2057
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 127

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.8_1069
PDB_EXTRACT data extraction version: 3.14
CrystalClear data collection
PHENIX phasing