X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 298.0
Details sodium cacodylate, MgCl2, PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.45 α = 90
b = 97.88 β = 90
c = 109.88 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 ADSC QUANTUM 315r Toroidal focusing mirror 2012-07-02
Diffraction Radiation
Monochromator Protocol
channel cut ESRF monochromator, Si(111) crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.93935 ESRF ID14-4

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
1.8 46.81 98.4 -- 0.181 -- 7.4 88436 88436 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)
1.8 1.9 97.2 -- 0.2228 1.4 7.6 12942

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 1.8 46.81 -- 1.35 88435 88435 2000 98.39 0.1837 0.1837 0.1827 0.225 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 1.8 1.845 -- 139 6016 0.3286 0.3728 -- 97.0
X Ray Diffraction 1.845 1.8949 -- 140 6048 0.281 0.3506 -- 97.0
X Ray Diffraction 1.8949 1.9507 -- 140 6044 0.2467 0.2881 -- 98.0
X Ray Diffraction 1.9507 2.0136 -- 140 6078 0.2155 0.2577 -- 98.0
X Ray Diffraction 2.0136 2.0856 -- 142 6109 0.2101 0.2531 -- 98.0
X Ray Diffraction 2.0856 2.1691 -- 141 6103 0.1972 0.2249 -- 98.0
X Ray Diffraction 2.1691 2.2678 -- 142 6122 0.1906 0.25 -- 98.0
X Ray Diffraction 2.2678 2.3874 -- 142 6147 0.1907 0.2529 -- 98.0
X Ray Diffraction 2.3874 2.5369 -- 143 6173 0.1872 0.2802 -- 99.0
X Ray Diffraction 2.5369 2.7328 -- 143 6208 0.1913 0.2512 -- 99.0
X Ray Diffraction 2.7328 3.0078 -- 144 6209 0.1978 0.2312 -- 99.0
X Ray Diffraction 3.0078 3.4429 -- 146 6282 0.1849 0.2173 -- 99.0
X Ray Diffraction 3.4429 4.3372 -- 145 6326 0.1453 0.176 -- 99.0
X Ray Diffraction 4.3372 46.8286 -- 153 6570 0.1396 0.1693 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_bond_d 0.007
f_angle_d 1.075
f_chiral_restr 0.046
f_dihedral_angle_d 13.273
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7296
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 411

Software

Software
Software Name Purpose
MxCuBE data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.4_1496)
XDS data reduction
XSCALE data scaling