X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 289.0
Details 0.1M sodium malonate, 12%(w/v) polyethylene glycol 3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.02 α = 90
b = 39.12 β = 110.64
c = 137.88 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 -- 2012-01-12
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.98 ALS 5.0.1

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
2.22 50 98.4 -- -- -- -- 28054 27608 2.0 2.0 46.26
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)
2.23 2.31 99.2 -- -- -- -- --

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
MOLECULAR REPLACEMENT 2.218 40.973 -- 1.35 28054 27608 1996 98.41 0.236 0.2371 0.2335 0.2827 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 2.2179 2.2733 -- 127 1652 0.339 0.3835 -- 90.0
X Ray Diffraction 2.2733 2.3348 -- 146 1806 0.3168 0.3686 -- 99.0
X Ray Diffraction 2.3348 2.4035 -- 131 1825 0.2962 0.3568 -- 99.0
X Ray Diffraction 2.4035 2.481 -- 147 1818 0.309 0.3746 -- 99.0
X Ray Diffraction 2.481 2.5697 -- 138 1839 0.3042 0.3635 -- 99.0
X Ray Diffraction 2.5697 2.6726 -- 144 1831 0.2732 0.391 -- 99.0
X Ray Diffraction 2.6726 2.7942 -- 138 1851 0.2879 0.3324 -- 99.0
X Ray Diffraction 2.7942 2.9415 -- 148 1819 0.2684 0.2892 -- 100.0
X Ray Diffraction 2.9415 3.1257 -- 150 1837 0.2678 0.294 -- 100.0
X Ray Diffraction 3.1257 3.3669 -- 133 1827 0.2316 0.267 -- 98.0
X Ray Diffraction 3.3669 3.7055 -- 151 1842 0.2292 0.2742 -- 99.0
X Ray Diffraction 3.7055 4.2413 -- 144 1870 0.2124 0.2549 -- 100.0
X Ray Diffraction 4.2413 5.3417 -- 148 1897 0.1888 0.247 -- 100.0
X Ray Diffraction 5.3417 40.9804 -- 151 1898 0.2 0.2524 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 83.6867
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.367
f_plane_restr 0.006
f_chiral_restr 0.079
f_angle_d 1.367
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3004
Nucleic Acid Atoms 486
Heterogen Atoms 0
Solvent Atoms 135

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
PHASES model building
HKL-2000 data collection