X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Microbatch Under Oil
pH 6.5
Temperature 277.0
Details protein buffer: 10 mM Tris HCl (pH 8). Precipitation cocktail: 100 MM NA CACODYLATE (PH 6.5), 5 mM FeCl2, 15% PEG 3350 Microbatch under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.16 α = 90
b = 79.68 β = 90
c = 83.78 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 MAR CCD 165 mm mirrors 2012-10-12
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.97012 NSLS X4C

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
1.4 31.02 99.9 0.059 0.041 -- 6.1 -- 61532 0.0 0.0 11.2
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 1.45 99.7 0.42 0.405 4.9 4.9 6060

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 1.4 31.021 1.3 1.34 61546 61460 6183 99.86 0.1394 0.1382 0.1349 0.1662 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 1.4003 1.4162 -- 198 1769 0.2995 0.3782 -- 98.0
X Ray Diffraction 1.4162 1.4328 -- 186 1808 0.247 0.2684 -- 100.0
X Ray Diffraction 1.4328 1.4503 -- 223 1820 0.2149 0.2578 -- 100.0
X Ray Diffraction 1.4503 1.4687 -- 193 1813 0.1738 0.1927 -- 100.0
X Ray Diffraction 1.4687 1.488 -- 206 1827 0.1662 0.22 -- 100.0
X Ray Diffraction 1.488 1.5084 -- 215 1799 0.1509 0.2006 -- 100.0
X Ray Diffraction 1.5084 1.5299 -- 221 1800 0.1451 0.1949 -- 100.0
X Ray Diffraction 1.5299 1.5528 -- 183 1852 0.127 0.1965 -- 100.0
X Ray Diffraction 1.5528 1.577 -- 195 1831 0.1196 0.1849 -- 100.0
X Ray Diffraction 1.577 1.6029 -- 201 1832 0.1158 0.1761 -- 100.0
X Ray Diffraction 1.6029 1.6305 -- 194 1831 0.1119 0.176 -- 100.0
X Ray Diffraction 1.6305 1.6602 -- 210 1841 0.1053 0.1594 -- 100.0
X Ray Diffraction 1.6602 1.6921 -- 191 1820 0.1064 0.1485 -- 100.0
X Ray Diffraction 1.6921 1.7266 -- 219 1824 0.1087 0.1667 -- 100.0
X Ray Diffraction 1.7266 1.7642 -- 215 1815 0.1009 0.1529 -- 100.0
X Ray Diffraction 1.7642 1.8052 -- 212 1861 0.1024 0.1566 -- 100.0
X Ray Diffraction 1.8052 1.8503 -- 201 1825 0.1057 0.1529 -- 100.0
X Ray Diffraction 1.8503 1.9004 -- 208 1824 0.1163 0.1458 -- 100.0
X Ray Diffraction 1.9004 1.9563 -- 214 1831 0.1185 0.166 -- 100.0
X Ray Diffraction 1.9563 2.0194 -- 209 1824 0.123 0.1618 -- 100.0
X Ray Diffraction 2.0194 2.0916 -- 195 1884 0.1238 0.1572 -- 100.0
X Ray Diffraction 2.0916 2.1753 -- 206 1850 0.1263 0.1547 -- 100.0
X Ray Diffraction 2.1753 2.2743 -- 184 1874 0.1231 0.155 -- 100.0
X Ray Diffraction 2.2743 2.3941 -- 216 1839 0.13 0.1599 -- 100.0
X Ray Diffraction 2.3941 2.5441 -- 202 1873 0.1331 0.1651 -- 100.0
X Ray Diffraction 2.5441 2.7404 -- 214 1849 0.1343 0.1642 -- 100.0
X Ray Diffraction 2.7404 3.0159 -- 204 1873 0.1401 0.1622 -- 100.0
X Ray Diffraction 3.0159 3.4519 -- 221 1890 0.1372 0.1501 -- 100.0
X Ray Diffraction 3.4519 4.3471 -- 212 1913 0.131 0.1447 -- 100.0
X Ray Diffraction 4.3471 31.0286 -- 235 1985 0.171 0.1719 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.2254
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.8007
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.4246
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.069
f_dihedral_angle_d 12.698
f_angle_d 1.148
f_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.13
Luzzati Sigma A (Observed) 0.09
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.13
Luzzati Sigma A (R-Free Set) 0.09
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2675
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 527

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
COMO Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
CNS1.3 refinement
XtalView refinement
COMO model building
ADSC version: Quantum data collection