X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.5
Temperature 298.0
Details PEG 3350, Bis-Tris HCl, NaCl, pH 5.5, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.38 α = 90
b = 40.26 β = 95.39
c = 84.46 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 -- 2012-01-28
Diffraction Radiation
Monochromator Protocol
LIQUID NITROGEN-COOLED DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.033 SSRL BL12-2

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
1.7 36.31 94.0 -- 0.075 -- 2.7 42465 42465 -- -3.0 --
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)
1.7 1.8 80.6 0.849 0.849 0.9 2.3 --

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 1.9 36.313 -- 1.35 32856 31363 1479 95.46 -- 0.1885 0.1868 0.2229 --
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 1.9 1.9613 -- 135 2719 0.2414 0.2916 -- 97.0
X Ray Diffraction 1.9613 2.0314 -- 134 2722 0.2183 0.2522 -- 95.0
X Ray Diffraction 2.0314 2.1128 -- 137 2743 0.2106 0.2406 -- 98.0
X Ray Diffraction 2.1128 2.2089 -- 134 2735 0.1958 0.236 -- 97.0
X Ray Diffraction 2.2089 2.3253 -- 134 2706 0.2033 0.2429 -- 96.0
X Ray Diffraction 2.3253 2.471 -- 134 2694 0.205 0.2209 -- 95.0
X Ray Diffraction 2.471 2.6617 -- 137 2776 0.2065 0.2619 -- 97.0
X Ray Diffraction 2.6617 2.9295 -- 134 2701 0.1996 0.2763 -- 95.0
X Ray Diffraction 2.9295 3.3531 -- 132 2685 0.1817 0.2147 -- 94.0
X Ray Diffraction 3.3531 4.2236 -- 134 2699 0.1615 0.2015 -- 94.0
X Ray Diffraction 4.2236 36.3198 -- 134 2704 0.1651 0.1777 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -6.1653
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.7781
Anisotropic B[2][2] 2.1845
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.9808
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.079
f_dihedral_angle_d 15.379
f_angle_d 1.234
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3360
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 305

Software

Computing
Computing Package Purpose
XDS Data Collection
XSCALE Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 3.3.16 data reduction