X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Crystallization Under Oil
pH 6.5
Temperature 277.0
Details 30% PEG 8000, 0.2M sodium acetate, 0.1M sodium cacodylate, pH 6.5, Microbatch crystallization under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.32 α = 90
b = 60.19 β = 90
c = 110.56 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-12-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.97921 APS 24-ID-E

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
1.74 40.58 100.0 0.089 -- -- 10.6 46740 46740 0.0 0.0 19.9
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)
1.739 1.85 99.9 0.949 -- 2.3 10.8 --

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
SAD 1.739 25.499 -- 1.21 -- 46732 2401 99.97 -- 0.1851 0.1843 0.1998 --
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 1.7395 1.775 -- 136 2618 0.3574 0.3743 -- 100.0
X Ray Diffraction 1.775 1.8136 -- 153 2570 0.3159 0.3085 -- 100.0
X Ray Diffraction 1.8136 1.8557 -- 116 2671 0.2712 0.2609 -- 100.0
X Ray Diffraction 1.8557 1.9021 -- 132 2564 0.2369 0.2694 -- 100.0
X Ray Diffraction 1.9021 1.9535 -- 140 2644 0.1976 0.2163 -- 100.0
X Ray Diffraction 1.9535 2.011 -- 150 2583 0.1907 0.1792 -- 100.0
X Ray Diffraction 2.011 2.0759 -- 160 2617 0.1844 0.203 -- 100.0
X Ray Diffraction 2.0759 2.15 -- 153 2567 0.1911 0.2169 -- 100.0
X Ray Diffraction 2.15 2.2361 -- 147 2607 0.1715 0.19 -- 100.0
X Ray Diffraction 2.2361 2.3378 -- 148 2621 0.1725 0.18 -- 100.0
X Ray Diffraction 2.3378 2.4609 -- 161 2560 0.177 0.1957 -- 100.0
X Ray Diffraction 2.4609 2.615 -- 137 2627 0.1759 0.2008 -- 100.0
X Ray Diffraction 2.615 2.8166 -- 139 2606 0.1768 0.1889 -- 100.0
X Ray Diffraction 2.8166 3.0997 -- 150 2603 0.1746 0.214 -- 100.0
X Ray Diffraction 3.0997 3.5472 -- 112 2650 0.1669 0.1928 -- 100.0
X Ray Diffraction 3.5472 4.4651 -- 145 2609 0.1522 0.1636 -- 100.0
X Ray Diffraction 4.4651 25.5022 -- 122 2614 0.184 0.1861 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -3.419
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.8031
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.3841
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.101
f_dihedral_angle_d 13.723
f_angle_d 1.471
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1964
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 178

Software

Computing
Computing Package Purpose
NE-CAT Remote Access Data Collection
XDS Data Reduction (intensity integration)
XScale Data Reduction (data scaling)
phenix.autosol Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
phenix refinement