X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 298.0
Details Bis-Tris pH 6.5, ammonium sulfate, PEG 3350, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 32.2 α = 108.54
b = 36.67 β = 90.3
c = 43.28 γ = 111.01
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-07-09
Diffraction Radiation
Monochromator Protocol
Sagitally focused Si MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537, 0.9797, 0.9795 AUSTRALIAN SYNCHROTRON MX2

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
1.25 32.14 99.9 0.08 -- -- 7.1 45786 45785 0.0 0.0 12.0
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)
1.4 1.47 92.4 0.58 -- 4.4 7.0 6572

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
MAD 1.4 27.724 -- 2.44 32997 32992 1676 96.52 -- 0.1395 0.1374 0.1772 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 1.4001 1.4413 -- 138 2458 0.142 0.2034 -- 92.0
X Ray Diffraction 1.4413 1.4878 -- 153 2577 0.1235 0.1813 -- 95.0
X Ray Diffraction 1.4878 1.541 -- 138 2606 0.1153 0.1827 -- 96.0
X Ray Diffraction 1.541 1.6027 -- 127 2603 0.1175 0.1748 -- 96.0
X Ray Diffraction 1.6027 1.6756 -- 127 2626 0.1246 0.193 -- 96.0
X Ray Diffraction 1.6756 1.7639 -- 136 2608 0.1289 0.1945 -- 97.0
X Ray Diffraction 1.7639 1.8744 -- 145 2623 0.131 0.1971 -- 97.0
X Ray Diffraction 1.8744 2.0191 -- 140 2631 0.1269 0.1818 -- 98.0
X Ray Diffraction 2.0191 2.2222 -- 137 2630 0.1266 0.1494 -- 98.0
X Ray Diffraction 2.2222 2.5436 -- 140 2657 0.13 0.1641 -- 98.0
X Ray Diffraction 2.5436 3.2039 -- 152 2684 0.1474 0.179 -- 99.0
X Ray Diffraction 3.2039 27.7293 -- 143 2613 0.1555 0.1766 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.6784
Anisotropic B[1][1] 0.0894
Anisotropic B[1][2] -0.0136
Anisotropic B[1][3] -0.1957
Anisotropic B[2][2] -0.3114
Anisotropic B[2][3] -0.6843
Anisotropic B[3][3] 0.222
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.934
f_plane_restr 0.007
f_chiral_restr 0.076
f_angle_d 1.303
f_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1587
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 202

Software

Computing
Computing Package Purpose
Blu-Ice GUI Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHARP Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SHARP phasing
SCALA data reduction