X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 297.0
Details 0.1M sodium citrate, 20% (w/v) PEG4000, 5% (v/v) 2-propanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.32 α = 90
b = 86.87 β = 126.02
c = 80.96 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirror 2013-02-04
Diffraction Radiation
Monochromator Protocol
Si 111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97929 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 40.5 96.0 0.118 -- -- 2.7 24439 24439 0.0 -3.0 --
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)
2.5 2.54 99.4 0.563 -- 3.1 2.7 1248

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 2.496 40.445 -- 1.34 24425 24425 1238 95.66 -- 0.1823 0.1799 0.2267 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 2.4957 2.5956 -- 155 2595 0.2288 0.2698 -- 96.0
X Ray Diffraction 2.5956 2.7137 -- 131 2661 0.2241 0.3115 -- 99.0
X Ray Diffraction 2.7137 2.8567 -- 149 2632 0.2226 0.2715 -- 99.0
X Ray Diffraction 2.8567 3.0356 -- 130 2660 0.216 0.3065 -- 99.0
X Ray Diffraction 3.0356 3.2699 -- 150 2650 0.1971 0.2643 -- 99.0
X Ray Diffraction 3.2699 3.5988 -- 134 2629 0.1754 0.2204 -- 98.0
X Ray Diffraction 3.5988 4.1191 -- 139 2554 0.1548 0.2142 -- 95.0
X Ray Diffraction 4.1191 5.1879 -- 129 2417 0.1472 0.1977 -- 89.0
X Ray Diffraction 5.1879 40.4499 -- 121 2389 0.1768 0.176 -- 87.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.044
f_dihedral_angle_d 13.036
f_angle_d 0.667
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5016
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 188

Software

Computing
Computing Package Purpose
SBC-Collect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
MolRep Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
MolRep model building
SBC-Collect data collection