X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 293.0
Details 22% Polyacrylic acid 5,100, 20 mM MgCl2, 100 mM CHES 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.82 α = 90
b = 89.82 β = 90
c = 316.2 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR DECTRIS PILATUS 6M -- 2012-09-20
Diffraction Radiation
Monochromator Protocol
Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 1.2395 BESSY 14.1

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
3.1 50 96.9 0.042 -- -- -- 51788 50204 -- -3.0 98.94
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)
3.1 3.2 98.5 0.562 -- 2.18 -- --

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 3.1 49.07 -- 1.98 51788 50204 2048 97.09 -- 0.2192 0.2161 0.2356 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 3.1005 3.178 -- 150 3426 0.3261 0.3425 -- 95.0
X Ray Diffraction 3.178 3.2639 -- 143 3492 0.3115 0.3483 -- 94.0
X Ray Diffraction 3.2639 3.3599 -- 152 3505 0.2945 0.3026 -- 95.0
X Ray Diffraction 3.3599 3.4684 -- 150 3505 0.2825 0.3151 -- 94.0
X Ray Diffraction 3.4684 3.5923 -- 152 3514 0.2735 0.2641 -- 94.0
X Ray Diffraction 3.5923 3.736 -- 141 3465 0.2624 0.2914 -- 94.0
X Ray Diffraction 3.736 3.9059 -- 139 3464 0.2537 0.2304 -- 94.0
X Ray Diffraction 3.9059 4.1117 -- 129 3425 0.2462 0.2537 -- 93.0
X Ray Diffraction 4.1117 4.3691 -- 141 3383 0.2288 0.258 -- 93.0
X Ray Diffraction 4.3691 4.7061 -- 138 3429 0.2166 0.2373 -- 91.0
X Ray Diffraction 4.7061 5.179 -- 127 3387 0.202 0.2438 -- 93.0
X Ray Diffraction 5.179 5.9267 -- 149 3447 0.2197 0.2619 -- 93.0
X Ray Diffraction 5.9267 7.4608 -- 137 3434 0.2155 0.2257 -- 93.0
X Ray Diffraction 7.4608 43.205 -- 149 3304 0.1534 0.1809 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 112.105
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.051
f_plane_restr 0.004
f_chiral_restr 0.057
f_angle_d 0.867
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16642
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.3.0 molecular replacement
Xscale data reduction