X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop Vapor Diffusion
pH 6.5
Temperature 293.0
Details 0.1 M MES, 0.8 M sodium acetate, 0.1 M NaCl, 20% (w/v) ethylene glycol, pH 6.5, hanging-drop vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117 α = 90
b = 46.89 β = 102.49
c = 57.47 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 315 monochromator 2012-10-18
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
synchrotron APS BEAMLINE 19-ID 0.97000 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
1.43 50 99.4 0.06 -- -- 3.7 53906 53906 1.0 1.0 --
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)
1.43 1.48 96.7 0.559 -- -- 3.2 --

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
FOURIER SYNTHESIS 1.4318 28.558 -- 1.36 53481 53888 2731 95.97 -- 0.1789 0.1773 0.2107 --
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 1.4318 1.4565 -- 43 808 0.298 0.3541 -- 31.0
X Ray Diffraction 1.4565 1.483 -- 144 2506 0.2573 0.2776 -- 95.0
X Ray Diffraction 1.483 1.5115 -- 152 2637 0.2394 0.2975 -- 99.0
X Ray Diffraction 1.5115 1.5424 -- 137 2631 0.2175 0.239 -- 100.0
X Ray Diffraction 1.5424 1.5759 -- 166 2645 0.2068 0.232 -- 100.0
X Ray Diffraction 1.5759 1.6126 -- 128 2681 0.203 0.2294 -- 100.0
X Ray Diffraction 1.6126 1.6529 -- 148 2617 0.1971 0.255 -- 100.0
X Ray Diffraction 1.6529 1.6976 -- 146 2639 0.1847 0.2437 -- 100.0
X Ray Diffraction 1.6976 1.7475 -- 152 2658 0.1847 0.23 -- 100.0
X Ray Diffraction 1.7475 1.8039 -- 120 2686 0.1873 0.2406 -- 100.0
X Ray Diffraction 1.8039 1.8684 -- 141 2630 0.1798 0.2321 -- 100.0
X Ray Diffraction 1.8684 1.9432 -- 148 2646 0.1769 0.2054 -- 100.0
X Ray Diffraction 1.9432 2.0316 -- 130 2659 0.1644 0.1938 -- 100.0
X Ray Diffraction 2.0316 2.1387 -- 143 2647 0.168 0.2031 -- 100.0
X Ray Diffraction 2.1387 2.2726 -- 144 2645 0.1608 0.1758 -- 100.0
X Ray Diffraction 2.2726 2.448 -- 141 2681 0.1603 0.1884 -- 100.0
X Ray Diffraction 2.448 2.6942 -- 151 2652 0.1673 0.1843 -- 100.0
X Ray Diffraction 2.6942 3.0836 -- 122 2706 0.1737 0.2067 -- 99.0
X Ray Diffraction 3.0836 3.8835 -- 139 2709 0.1732 0.207 -- 100.0
X Ray Diffraction 3.8835 28.5634 -- 136 2674 0.1775 0.2144 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.5903
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.076
f_dihedral_angle_d 12.104
f_angle_d 1.28
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2505
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 256

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction