X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details 1.5-4 % PEG8000, 50 mM MES, 100 mM Glycine, 1 mM ATP, 1 mM Valine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.57 α = 90
b = 92.57 β = 90
c = 164.39 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD SSRL. 2010-07-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2

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
2.15 30 92.9 0.087 -- -- -- 39581 36771 -- -3.0 29.5
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)
2.15 2.25 97.9 0.481 -- -- -- --

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 2.15 29.38 -- 1.33 39578 36768 1862 92.83 -- 0.1885 0.1861 0.2338 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 2.15 2.2081 -- 142 2771 0.2318 0.2876 -- 98.0
X Ray Diffraction 2.2081 2.2731 -- 142 2169 0.3633 0.5066 -- 77.0
X Ray Diffraction 2.2731 2.3464 -- 122 2776 0.2535 0.2953 -- 97.0
X Ray Diffraction 2.3464 2.4302 -- 147 2794 0.1973 0.2766 -- 98.0
X Ray Diffraction 2.4302 2.5275 -- 143 2773 0.188 0.2279 -- 97.0
X Ray Diffraction 2.5275 2.6424 -- 144 2777 0.2066 0.2535 -- 97.0
X Ray Diffraction 2.6424 2.7817 -- 161 2586 0.2251 0.2769 -- 91.0
X Ray Diffraction 2.7817 2.9558 -- 138 2779 0.1926 0.2578 -- 97.0
X Ray Diffraction 2.9558 3.1838 -- 162 2785 0.1734 0.2144 -- 96.0
X Ray Diffraction 3.1838 3.5037 -- 160 2526 0.1816 0.2635 -- 88.0
X Ray Diffraction 3.5037 4.0096 -- 118 2459 0.1768 0.2332 -- 84.0
X Ray Diffraction 4.0096 5.0475 -- 135 2817 0.1408 0.1653 -- 94.0
X Ray Diffraction 5.0475 29.3826 -- 148 2894 0.165 0.159 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.4555
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.4555
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.9111
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_dihedral_angle_d 12.669
f_angle_d 1.27
f_chiral_restr 0.095
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3776
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 245

Software

Software
Software Name Purpose
Blu-Ice data collection
MOLREP phasing
PHENIX refinement version: (phenix.refine: 1.7.1_743)
HKL-2000 data reduction
HKL-2000 data scaling