X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.2
Temperature 295.0
Details 0.1 M Na citrate, 25% PEG 4000, 20% isopropanol. 0.2 M ammonium acetate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.2 α = 90
b = 45.2 β = 90
c = 247.1 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2010-10-13
Diffraction Radiation
Monochromator Protocol
DCM MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9793 CLSI 08ID-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
1.4 41.18 96.7 0.054 -- -- 6.9 -- 57398 -- -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)
1.4 1.44 77.2 0.773 -- 2.06 -- --

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 1.4 41.183 -- 1.99 -- 57397 1988 96.68 -- 0.152 0.1514 0.1692 --
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 1.4004 1.4355 -- 110 3031 0.2443 0.2596 -- 77.0
X Ray Diffraction 1.4355 1.4743 -- 126 3446 0.214 0.2394 -- 85.0
X Ray Diffraction 1.4743 1.5177 -- 140 3915 0.1903 0.2352 -- 97.0
X Ray Diffraction 1.5177 1.5666 -- 144 4004 0.1681 0.1818 -- 99.0
X Ray Diffraction 1.5666 1.6226 -- 137 3948 0.164 0.1982 -- 99.0
X Ray Diffraction 1.6226 1.6876 -- 147 3993 0.1489 0.1872 -- 99.0
X Ray Diffraction 1.6876 1.7644 -- 141 3992 0.1456 0.1824 -- 99.0
X Ray Diffraction 1.7644 1.8574 -- 147 4040 0.1455 0.1615 -- 99.0
X Ray Diffraction 1.8574 1.9738 -- 145 4076 0.1431 0.1521 -- 99.0
X Ray Diffraction 1.9738 2.1262 -- 143 4063 0.1359 0.1449 -- 100.0
X Ray Diffraction 2.1262 2.3402 -- 148 4101 0.1342 0.1735 -- 100.0
X Ray Diffraction 2.3402 2.6787 -- 149 4152 0.1396 0.1571 -- 100.0
X Ray Diffraction 2.6787 3.3747 -- 150 4189 0.145 0.1576 -- 100.0
X Ray Diffraction 3.3747 41.2011 -- 161 4459 0.1556 0.1631 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.73
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_dihedral_angle_d 11.474
f_chiral_restr 0.115
f_angle_d 1.397
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2334
Nucleic Acid Atoms 0
Heterogen Atoms 166
Solvent Atoms 429

Software

Software
Software Name Purpose
XDS data reduction version: March 5, 2012
XSCALE data scaling
PHASER phasing
PHENIX refinement version: dev_1034
PDB_EXTRACT data extraction version: 3.20