X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 277.0
Details 2.0 M ammonium sulfate, and 0.1 M Tris.HCl pH 8.5, vapor diffusion, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.96 α = 90
b = 105.96 β = 90
c = 84.25 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2010-07-29
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 1.03299 APS 23-ID-D

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
1.9 50 99.8 0.082 -- -- 6.9 22523 22478 0.0 0.0 --
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)
1.9 1.97 98.5 0.672 -- -- 3.7 2162

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 40.293 -- 0.14 22535 20022 1018 95.91 0.207 0.1889 0.1862 0.2441 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 2.0528 -- 137 -- 0.1962 0.2535 -- 89.0
X Ray Diffraction 2.0528 2.1814 -- 154 -- 0.1737 0.2386 -- 93.0
X Ray Diffraction 2.1814 2.3499 -- 158 -- 0.1791 0.2352 -- 95.0
X Ray Diffraction 2.3499 2.5863 -- 152 -- 0.1729 0.2456 -- 97.0
X Ray Diffraction 2.5863 2.9604 -- 161 -- 0.188 0.2743 -- 98.0
X Ray Diffraction 2.9604 3.7294 -- 113 -- 0.1705 0.2355 -- 99.0
X Ray Diffraction 3.7294 40.3016 -- 143 -- 0.1955 0.2239 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.0483
Anisotropic B[1][1] -1.9664
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.9664
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.9329
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.01
f_chiral_restr 0.123
f_dihedral_angle_d 27.904
f_angle_d 1.552
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1915
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 179

Software

Computing
Computing Package Purpose
BluIce Epics Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.6_289) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
HKL data reduction