X-RAY DIFFRACTION Experimental Data & Validation


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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 = 54.61 α = 90
b = 81.4 β = 109.94
c = 58.41 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 -- 2011-12-14
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 0.9 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 98.55 -- 0.138 -- 3.3 21406 21406 1.0 1.0 28.4
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 98.85 -- 0.0 -- 3.0 21406

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 2.29 40.159 -- 0.0 20231 20231 1199 93.14 0.1964 0.1964 0.1939 0.2367 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 2.29 2.3818 -- 119 1965 0.2365 0.3152 -- 87.0
X Ray Diffraction 2.3818 2.4902 -- 134 1993 0.2324 0.2729 -- 89.0
X Ray Diffraction 2.4902 2.6215 -- 126 2049 0.2289 0.315 -- 91.0
X Ray Diffraction 2.6215 2.7857 -- 132 2060 0.2186 0.2758 -- 91.0
X Ray Diffraction 2.7857 3.0007 -- 132 2103 0.211 0.2542 -- 93.0
X Ray Diffraction 3.0007 3.3025 -- 135 2174 0.2006 0.2441 -- 96.0
X Ray Diffraction 3.3025 3.7801 -- 143 2194 0.1824 0.2158 -- 97.0
X Ray Diffraction 3.7801 4.7613 -- 137 2216 0.1509 0.1876 -- 97.0
X Ray Diffraction 4.7613 40.159 -- 141 2278 0.1953 0.2222 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.352
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.0447
Anisotropic B[2][2] 3.0794
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.7274
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.001
f_chiral_restr 0.033
f_dihedral_angle_d 12.762
f_angle_d 0.452
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3908
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 184

Software

Computing
Computing Package Purpose
Blu 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
Blu version: Ice data collection