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 = 54.48 α = 90
b = 81.4 β = 109.82
c = 58.6 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
2.06 50 97.16 -- 0.114 -- 6.5 29295 29295 1.0 1.0 37.59
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)
2.06 2.1 90.58 -- 0.0 2.36 6.2 --

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 2.06 46.141 -- 0.0 27983 27983 1906 92.81 0.1876 0.1876 0.1846 0.2295 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 2.06 2.1042 -- 109 1528 0.2571 0.3626 -- 76.0
X Ray Diffraction 2.1042 2.1611 -- 127 1698 0.2189 0.2617 -- 86.0
X Ray Diffraction 2.1611 2.2247 -- 128 1720 0.2035 0.2589 -- 86.0
X Ray Diffraction 2.2247 2.2965 -- 129 1843 0.1987 0.2379 -- 93.0
X Ray Diffraction 2.2965 2.3786 -- 134 1885 0.2061 0.2587 -- 93.0
X Ray Diffraction 2.3786 2.4738 -- 142 1875 0.2031 0.2453 -- 94.0
X Ray Diffraction 2.4738 2.5864 -- 148 1902 0.2055 0.2898 -- 96.0
X Ray Diffraction 2.5864 2.7227 -- 140 1919 0.2113 0.2658 -- 95.0
X Ray Diffraction 2.7227 2.8933 -- 135 1879 0.213 0.2488 -- 94.0
X Ray Diffraction 2.8933 3.1166 -- 145 1964 0.1997 0.2379 -- 98.0
X Ray Diffraction 3.1166 3.4302 -- 142 1972 0.194 0.2749 -- 98.0
X Ray Diffraction 3.4302 3.9263 -- 143 1943 0.1658 0.2182 -- 97.0
X Ray Diffraction 3.9263 4.9458 -- 136 1941 0.1443 0.1741 -- 95.0
X Ray Diffraction 4.9458 46.141 -- 148 2008 0.1829 0.2052 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.2459
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.0084
Anisotropic B[2][2] 3.6704
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.4245
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.053
f_dihedral_angle_d 14.505
f_angle_d 0.787
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3843
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 138

Software

Computing
Computing Package Purpose
Blue ice 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
Blue version: ice data collection