X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 298.0
Details 0.9 M sodium citrate, 0.1 M imidazole, and 25 mM 2-mercaptoethanol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.48 α = 90
b = 110.35 β = 90
c = 119.84 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 MARMOSAIC 225 mm CCD -- 2010-03-15
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
1.58 50 98.4 0.103 0.103 -- 12.4 121024 121024 -- -3.0 --
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)
1.58 1.61 86.0 0.442 0.442 2.1 4.9 5211

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 1.58 40.234 -- 0.0 -- 120904 6055 98.3 -- 0.1573 0.1557 0.1887 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 1.5796 1.5976 3398 196 3202 0.2578 0.2983 -- 84.0
X Ray Diffraction 1.5976 1.6163 3594 173 3421 0.2661 0.2904 -- 88.0
X Ray Diffraction 1.6163 1.6361 3683 189 3494 0.2278 0.2616 -- 91.0
X Ray Diffraction 1.6361 1.6568 3797 175 3622 0.2135 0.2297 -- 93.0
X Ray Diffraction 1.6568 1.6786 3895 191 3704 0.2038 0.2506 -- 96.0
X Ray Diffraction 1.6786 1.7016 3937 213 3724 0.1823 0.2262 -- 98.0
X Ray Diffraction 1.7016 1.7259 4020 199 3821 0.1738 0.2072 -- 99.0
X Ray Diffraction 1.7259 1.7516 4042 210 3832 0.167 0.2082 -- 100.0
X Ray Diffraction 1.7516 1.779 4097 204 3893 0.1616 0.1762 -- 100.0
X Ray Diffraction 1.779 1.8082 4046 197 3849 0.1625 0.2231 -- 100.0
X Ray Diffraction 1.8082 1.8394 4067 204 3863 0.1569 0.2123 -- 100.0
X Ray Diffraction 1.8394 1.8728 4097 196 3901 0.1578 0.2094 -- 100.0
X Ray Diffraction 1.8728 1.9088 4017 198 3819 0.1545 0.2009 -- 100.0
X Ray Diffraction 1.9088 1.9478 4053 200 3853 0.1582 0.2063 -- 100.0
X Ray Diffraction 1.9478 1.9901 4112 207 3905 0.154 0.2077 -- 100.0
X Ray Diffraction 1.9901 2.0364 4058 206 3852 0.152 0.1919 -- 100.0
X Ray Diffraction 2.0364 2.0873 4071 194 3877 0.1536 0.1765 -- 100.0
X Ray Diffraction 2.0873 2.1438 4101 210 3891 0.1485 0.1847 -- 100.0
X Ray Diffraction 2.1438 2.2069 4107 210 3897 0.1522 0.1774 -- 100.0
X Ray Diffraction 2.2069 2.2781 4059 208 3851 0.1533 0.1895 -- 100.0
X Ray Diffraction 2.2781 2.3595 4116 215 3901 0.1559 0.1826 -- 100.0
X Ray Diffraction 2.3595 2.454 4109 188 3921 0.1472 0.184 -- 100.0
X Ray Diffraction 2.454 2.5656 4090 207 3883 0.1528 0.2071 -- 100.0
X Ray Diffraction 2.5656 2.7009 4127 211 3916 0.1576 0.183 -- 100.0
X Ray Diffraction 2.7009 2.87 4114 197 3917 0.1622 0.1851 -- 100.0
X Ray Diffraction 2.87 3.0916 4153 203 3950 0.1566 0.1958 -- 100.0
X Ray Diffraction 3.0916 3.4025 4159 212 3947 0.1467 0.1549 -- 100.0
X Ray Diffraction 3.4025 3.8945 4171 214 3957 0.1264 0.1564 -- 100.0
X Ray Diffraction 3.8945 4.9053 4231 204 4027 0.1231 0.1498 -- 100.0
X Ray Diffraction 4.9053 40.2468 4383 224 4159 0.1567 0.1805 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.3122
Anisotropic B[1][1] -2.2324
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.0437
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.8113
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.507
f_plane_restr 0.005
f_chiral_restr 0.074
f_angle_d 1.068
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7768
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 1272

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction