X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 293.0
Details 50 mM NaCl, 0.3 mM tris(2-carboxyethyl)phosphine, 10 mM HEPES-NaOH (pH 7.8), 25% polyethylene glycol 3350, 200 mM sodium chloride, 40 mM glycine, 100 mM BIS-TRIS-HCl, (pH 5.5), vapor diffusion, sitting drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.04 α = 90
b = 47.04 β = 90
c = 125.97 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors 2012-01-01
Diffraction Radiation
Monochromator Protocol
-- Single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
synchrotron APS BEAMLINE 21-ID-D 0.97895 APS 21-ID-D

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
1.77 50 99.8 0.069 -- -- 10.0 14559 14530 0.0 0.0 --
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)
1.77 1.8 98.5 0.323 -- -- 9.5 699

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 1.772 44.068 -- 0.0 14498 14336 1437 98.88 0.159 0.159 0.1546 0.1996 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 1.7718 1.8352 -- 136 1206 0.1646 0.2259 -- 96.0
X Ray Diffraction 1.8352 1.9086 -- 136 1227 0.1587 0.2188 -- 97.0
X Ray Diffraction 1.9086 1.9955 -- 140 1257 0.146 0.1876 -- 99.0
X Ray Diffraction 1.9955 2.1007 -- 143 1270 0.1456 0.2078 -- 99.0
X Ray Diffraction 2.1007 2.2323 -- 141 1282 0.1413 0.1905 -- 100.0
X Ray Diffraction 2.2323 2.4047 -- 142 1270 0.1566 0.2203 -- 100.0
X Ray Diffraction 2.4047 2.6466 -- 144 1299 0.1707 0.2091 -- 100.0
X Ray Diffraction 2.6466 3.0295 -- 146 1312 0.17 0.1986 -- 100.0
X Ray Diffraction 3.0295 3.8166 -- 148 1333 0.1421 0.191 -- 100.0
X Ray Diffraction 3.8166 44.0812 -- 161 1443 0.1559 0.1916 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.2812
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.122
f_plane_restr 0.005
f_chiral_restr 0.083
f_angle_d 1.264
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1201
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 137

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.5.0 molecular replacement
HKL data reduction