X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 289.0
Details 24 % Polyvinylpyrrolidone, 50 mM Hepes pH 8.0, 100 mM sodium chloride, 10 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.43 α = 90
b = 92.43 β = 90
c = 96.37 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2012-11-02
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97910 APS 19-ID

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
2.5 50 99.7 -- 0.057 -- 4.0 31681 31681 0.0 0.0 58.8
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)
2.5 2.54 99.4 -- 0.744 1.9 3.6 1563

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 2.502 30.786 -- 0.0 31655 31655 1595 99.69 0.185 0.185 0.182 0.224 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 2.502 2.5827 2859 152 2707 0.2668 0.3271 -- 99.0
X Ray Diffraction 2.5827 2.6749 2872 134 2738 0.2457 0.2651 -- 100.0
X Ray Diffraction 2.6749 2.782 2910 141 2769 0.2337 0.258 -- 100.0
X Ray Diffraction 2.782 2.9085 2868 132 2736 0.2382 0.3325 -- 100.0
X Ray Diffraction 2.9085 3.0617 2891 141 2750 0.2284 0.3097 -- 100.0
X Ray Diffraction 3.0617 3.2533 2853 143 2720 0.2305 0.278 -- 100.0
X Ray Diffraction 3.2533 3.5042 2915 142 2773 0.2003 0.2454 -- 100.0
X Ray Diffraction 3.5042 3.8562 2875 144 2732 0.1752 0.2027 -- 100.0
X Ray Diffraction 3.8562 4.4128 2857 158 2699 0.1533 0.1888 -- 100.0
X Ray Diffraction 4.4128 5.5544 2894 170 2724 0.1484 0.1948 -- 100.0
X Ray Diffraction 5.5544 30.7887 2850 138 2712 0.1629 0.2033 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model mixed
Mean Isotropic B 64.5
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.046
f_dihedral_angle_d 17.198
f_angle_d 0.686
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4828
Nucleic Acid Atoms 856
Heterogen Atoms 23
Solvent Atoms 159

Software

Computing
Computing Package Purpose
SBCCOLLECT, HKL3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL3000, Molrep Structure Solution
PHENIX (phenix.refine: 1.8.1_1161) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1161) refinement
Molrep model building
HKL3000 model building
HKL3000 data collection
SBCCOLLECT data collection