X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 289.0
Details 25 % PEG 4000, 50 mM Tris pH 7.5, 160 mM sodium formate, 10 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.93 α = 90
b = 92.93 β = 90
c = 97.65 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 2010-12-10
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
3 50 100.0 -- 0.157 -- 6.8 18807 18807 0.0 0.0 55.5
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)
3.0 3.05 100.0 -- 0.709 2.0 5.4 905

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 3.004 46.465 -- 0.0 18786 18786 965 100.0 0.177 0.177 0.168 0.205 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 3.0039 3.1622 2654 143 2511 0.2032 0.2183 -- 95.0
X Ray Diffraction 3.1622 3.3602 2696 151 2545 0.1842 0.229 -- 94.0
X Ray Diffraction 3.3602 3.6195 2697 146 2551 0.1737 0.2281 -- 95.0
X Ray Diffraction 3.6195 3.9833 2665 140 2525 0.1677 0.1994 -- 95.0
X Ray Diffraction 3.9833 4.5588 2687 147 2540 0.1577 0.192 -- 95.0
X Ray Diffraction 4.5588 5.7403 2689 133 2556 0.1643 0.1848 -- 95.0
X Ray Diffraction 5.7403 37.2077 2692 105 2587 0.1872 0.2344 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model mixed
Mean Isotropic B 57.9
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.049
f_dihedral_angle_d 19.606
f_angle_d 0.761
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4872
Nucleic Acid Atoms 978
Heterogen Atoms 1
Solvent Atoms 26

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), refmac5.5 Structure Refinement
Software
Software Name Purpose
refmac5.5 refinement
PHENIX version: (phenix.refine: 1.8.1_1161) refinement
Molrep model building
HKL3000 model building
HKL3000 data collection
SBCCOLLECT data collection