X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 13-18% PEG 3350, 0.015 mM Tris pH 8 and 0.4 M NaI

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.84 α = 90
b = 66.61 β = 90
c = 144.48 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX300HE -- 2014-09-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08B1-1 0.9796 CLSI 08B1-1

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 39.03 100.0 0.092 -- -- 7.3 -- 41021 -- -3.0 24.89
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 1.95 100.0 0.834 -- 2.58 -- --

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
FOURIER SYNTHESIS 1.9 39.028 -- 1.36 -- 41015 2050 99.97 -- 0.1824 0.1805 0.2194 --
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 1.9442 -- 133 2541 0.2795 0.3513 -- 100.0
X Ray Diffraction 1.9442 1.9928 -- 134 2547 0.247 0.265 -- 100.0
X Ray Diffraction 1.9928 2.0467 -- 136 2574 0.22 0.2183 -- 100.0
X Ray Diffraction 2.0467 2.1069 -- 135 2564 0.2148 0.2314 -- 100.0
X Ray Diffraction 2.1069 2.1749 -- 134 2546 0.2042 0.2781 -- 100.0
X Ray Diffraction 2.1749 2.2527 -- 135 2561 0.2008 0.2215 -- 100.0
X Ray Diffraction 2.2527 2.3428 -- 135 2562 0.1889 0.2488 -- 100.0
X Ray Diffraction 2.3428 2.4495 -- 137 2604 0.1838 0.2396 -- 100.0
X Ray Diffraction 2.4495 2.5786 -- 136 2592 0.1882 0.2067 -- 100.0
X Ray Diffraction 2.5786 2.7401 -- 136 2579 0.1869 0.2407 -- 100.0
X Ray Diffraction 2.7401 2.9516 -- 137 2599 0.1907 0.2374 -- 100.0
X Ray Diffraction 2.9516 3.2485 -- 137 2603 0.1767 0.2475 -- 100.0
X Ray Diffraction 3.2485 3.7182 -- 139 2641 0.1664 0.2141 -- 100.0
X Ray Diffraction 3.7182 4.6833 -- 139 2657 0.1387 0.1725 -- 100.0
X Ray Diffraction 4.6833 39.0358 -- 147 2795 0.1737 0.1878 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.7862
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.051
f_bond_d 0.009
f_angle_d 1.203
f_plane_restr 0.006
f_dihedral_angle_d 14.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3393
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 284

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.15
XDS data reduction
PHENIX phasing