X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details PEG 4000 isopropanol, pH 7.5, sitting-drop vapor diffusion, temperature 100K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.62 α = 90
b = 63.62 β = 90
c = 155.2 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 345 mm plate -- 2012-01-01
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.97 APS 14-BM-C

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
1.77 50 99.8 0.045 -- -- 11.0 -- 18791 -- -- --
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)
1.77 1.83 100.0 0.258 -- -- 11.2 --

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 1.77 31.809 -- 1.34 -- 18783 939 99.21 -- 0.193 0.1908 0.2346 --
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 1.7699 1.8632 -- 127 2463 0.2433 0.3277 -- 99.0
X Ray Diffraction 1.8632 1.9799 -- 130 2476 0.2065 0.2232 -- 99.0
X Ray Diffraction 1.9799 2.1327 -- 132 2496 0.202 0.2445 -- 99.0
X Ray Diffraction 2.1327 2.3473 -- 133 2522 0.2009 0.2708 -- 100.0
X Ray Diffraction 2.3473 2.6868 -- 135 2542 0.2033 0.2724 -- 100.0
X Ray Diffraction 2.6868 3.3845 -- 137 2596 0.183 0.201 -- 100.0
X Ray Diffraction 3.3845 31.8146 -- 145 2749 0.1731 0.2114 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model mixed isotropic/anisotropic
Anisotropic B[1][1] 1.928
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.928
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.8561
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.04
f_dihedral_angle_d 12.328
f_angle_d 0.673
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1463
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 310

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALEPACK data reduction
DENZO data collection