X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 277.0
Details 0.016 M NiCl2, 0.1 M Tris-HCl, 16% polyethylene glycol monomethyl ether 2000, and 0.13 M glycine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 27.92 α = 90
b = 77.09 β = 96.01
c = 95.18 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 MARMOSAIC 225 mm CCD -- 2009-12-17
CCD MARMOSAIC 225 mm CCD -- 2010-04-12
Diffraction Radiation
Monochromator Protocol
-- --
-- --
Si(111) MAD
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.9796 APS 22-BM
SYNCHROTRON APS BEAMLINE 22-BM 0.9794 APS 22-BM
SYNCHROTRON APS BEAMLINE 22-BM 0.9719 APS 22-BM
SYNCHROTRON APS BEAMLINE 22-BM 1.0001 APS 22-BM

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 98.3 -- -- -- -- 27256 26788 2.0 2.0 --
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)
2.0 2.03 99.4 0.134 -- 11.7 4.1 --

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
MAD 2.0 24.797 -- 0.0 27256 26272 1314 96.45 -- 0.1919 0.1892 0.2408 --
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 1.9972 2.0772 -- 133 2693 0.1957 0.288 -- 96.0
X Ray Diffraction 2.0772 2.1716 -- 149 2804 0.1785 0.2306 -- 97.0
X Ray Diffraction 2.1716 2.2861 -- 109 2509 0.2025 0.2782 -- 87.0
X Ray Diffraction 2.2861 2.4292 -- 140 2774 0.1862 0.242 -- 97.0
X Ray Diffraction 2.4292 2.6165 -- 153 2849 0.2057 0.2435 -- 99.0
X Ray Diffraction 2.6165 2.8795 -- 144 2859 0.2087 0.2486 -- 99.0
X Ray Diffraction 2.8795 3.2953 -- 154 2868 0.1988 0.2386 -- 100.0
X Ray Diffraction 3.2953 4.1486 -- 154 2709 0.1728 0.2409 -- 94.0
X Ray Diffraction 4.1486 24.7991 -- 178 2893 0.1779 0.2188 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.2353
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.3241
Anisotropic B[2][2] -5.1785
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.9432
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.065
f_dihedral_angle_d 12.925
f_angle_d 0.917
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3193
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 502

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0072 refinement
SOLVE model building
HKL-2000 data collection