X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 294.0
Details 15% PEG 3350, 0.05M magnesium chloride, 0.067M sodium chloride, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.73 α = 90
b = 81.63 β = 109.77
c = 58.47 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
PIXEL DECTRIS PILATUS 6M -- 2012-07-27
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube I-beam single crystal, asymmetric cut 4.965 degs SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.0 SSRL BL11-1

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
1.98 50 97.76 -- 0.076 -- 6.6 33288 33288 1.0 1.0 32.69
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)
1.98 2.01 93.74 -- 0.643 2.54 6.6 --

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 1.98 46.197 -- 0.0 31685 31685 1903 93.05 0.1838 0.1838 0.181 0.2268 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 1.98 2.024 -- 117 1822 0.2376 0.2858 -- 80.0
X Ray Diffraction 2.024 2.0787 -- 118 2011 0.2081 0.3309 -- 88.0
X Ray Diffraction 2.0787 2.1398 -- 132 2032 0.2134 0.2799 -- 90.0
X Ray Diffraction 2.1398 2.2089 -- 127 1999 0.2016 0.2858 -- 88.0
X Ray Diffraction 2.2089 2.2879 -- 127 2010 0.2289 0.3288 -- 88.0
X Ray Diffraction 2.2879 2.3795 -- 145 2159 0.1992 0.2397 -- 94.0
X Ray Diffraction 2.3795 2.4877 -- 136 2186 0.1885 0.2616 -- 97.0
X Ray Diffraction 2.4877 2.6189 -- 139 2213 0.1889 0.2299 -- 97.0
X Ray Diffraction 2.6189 2.783 -- 141 2196 0.1987 0.2146 -- 96.0
X Ray Diffraction 2.783 2.9978 -- 141 2191 0.1935 0.2589 -- 97.0
X Ray Diffraction 2.9978 3.2994 -- 136 2266 0.1904 0.2649 -- 99.0
X Ray Diffraction 3.2994 3.7766 -- 146 2202 0.1711 0.1939 -- 96.0
X Ray Diffraction 3.7766 4.7574 -- 146 2204 0.1386 0.1814 -- 96.0
X Ray Diffraction 4.7574 46.197 -- 152 2291 0.1799 0.2074 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.0241
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.1554
Anisotropic B[2][2] 2.7606
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7364
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.06
f_dihedral_angle_d 13.684
f_angle_d 0.91
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3845
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 197

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.automr) Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX version: (phenix.automr) model building
HKL-2000 data collection