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 = 54.24 α = 90
b = 80.81 β = 109.81
c = 57.9 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 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
1.9 50 98.21 -- 0.073 -- 3.4 25549 25549 1.0 1.0 31.67
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 1.93 95.12 -- 0.0 2.06 3.2 --

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 2.14 39.829 -- 0.0 24264 24264 1319 93.27 0.1801 0.1801 0.1775 0.2256 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 2.14 2.2257 -- 117 2246 0.2312 0.2762 -- 82.0
X Ray Diffraction 2.2257 2.327 -- 146 2404 0.1997 0.2829 -- 89.0
X Ray Diffraction 2.327 2.4496 -- 141 2487 0.1898 0.2045 -- 92.0
X Ray Diffraction 2.4496 2.6031 -- 136 2566 0.1915 0.2666 -- 93.0
X Ray Diffraction 2.6031 2.804 -- 156 2496 0.2018 0.2603 -- 92.0
X Ray Diffraction 2.804 3.0861 -- 157 2638 0.1958 0.2464 -- 97.0
X Ray Diffraction 3.0861 3.5324 -- 152 2683 0.1786 0.2327 -- 98.0
X Ray Diffraction 3.5324 4.4495 -- 152 2675 0.1469 0.1871 -- 97.0
X Ray Diffraction 4.4495 39.829 -- 162 2750 0.1701 0.2078 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.1215
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.0025
Anisotropic B[2][2] 3.8134
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.6919
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.051
f_dihedral_angle_d 14.465
f_angle_d 0.728
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3841
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 161

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