X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.65 α = 90
b = 95.76 β = 90
c = 137.39 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2012-08-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 1.03 APS 23-ID-D

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
1.39 50 99.2 0.084 -- -- 9.5 -- 107340 -- -- --
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)
1.39 1.44 98.1 0.718 -- -- 7.2 10486

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 1.39 47.882 -- 1.33 -- 107253 5352 99.06 -- 0.1322 0.1311 0.1529 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 1.39 1.4047 -- 151 3279 0.1835 0.2258 -- 96.0
X Ray Diffraction 1.4047 1.4212 -- 162 3312 0.1725 0.2059 -- 98.0
X Ray Diffraction 1.4212 1.4385 -- 175 3335 0.1528 0.1858 -- 98.0
X Ray Diffraction 1.4385 1.4567 -- 178 3366 0.1477 0.1759 -- 98.0
X Ray Diffraction 1.4567 1.4759 -- 176 3303 0.1408 0.201 -- 98.0
X Ray Diffraction 1.4759 1.4961 -- 166 3368 0.1316 0.1704 -- 98.0
X Ray Diffraction 1.4961 1.5175 -- 193 3307 0.1268 0.172 -- 98.0
X Ray Diffraction 1.5175 1.5402 -- 169 3366 0.1168 0.1525 -- 99.0
X Ray Diffraction 1.5402 1.5642 -- 197 3313 0.1161 0.155 -- 99.0
X Ray Diffraction 1.5642 1.5899 -- 172 3354 0.1085 0.1439 -- 99.0
X Ray Diffraction 1.5899 1.6173 -- 177 3360 0.1075 0.1438 -- 99.0
X Ray Diffraction 1.6173 1.6467 -- 188 3387 0.1113 0.142 -- 99.0
X Ray Diffraction 1.6467 1.6784 -- 177 3361 0.1128 0.1533 -- 99.0
X Ray Diffraction 1.6784 1.7126 -- 169 3397 0.113 0.1646 -- 99.0
X Ray Diffraction 1.7126 1.7499 -- 173 3395 0.1154 0.1612 -- 99.0
X Ray Diffraction 1.7499 1.7906 -- 169 3405 0.1105 0.1573 -- 99.0
X Ray Diffraction 1.7906 1.8354 -- 179 3366 0.1084 0.1494 -- 99.0
X Ray Diffraction 1.8354 1.885 -- 170 3419 0.1133 0.1577 -- 99.0
X Ray Diffraction 1.885 1.9405 -- 158 3432 0.1173 0.1483 -- 100.0
X Ray Diffraction 1.9405 2.0031 -- 201 3375 0.1164 0.1541 -- 100.0
X Ray Diffraction 2.0031 2.0747 -- 167 3426 0.1151 0.1324 -- 100.0
X Ray Diffraction 2.0747 2.1578 -- 178 3431 0.1196 0.1581 -- 100.0
X Ray Diffraction 2.1578 2.256 -- 197 3415 0.1184 0.1492 -- 100.0
X Ray Diffraction 2.256 2.3749 -- 173 3440 0.1209 0.1539 -- 100.0
X Ray Diffraction 2.3749 2.5237 -- 189 3452 0.1276 0.1297 -- 100.0
X Ray Diffraction 2.5237 2.7185 -- 187 3439 0.1292 0.1437 -- 100.0
X Ray Diffraction 2.7185 2.9921 -- 175 3489 0.1338 0.1507 -- 100.0
X Ray Diffraction 2.9921 3.4249 -- 205 3451 0.139 0.1661 -- 100.0
X Ray Diffraction 3.4249 4.3146 -- 195 3508 0.1379 0.1262 -- 100.0
X Ray Diffraction 4.3146 47.882 -- 186 3650 0.1663 0.1714 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.6919
Anisotropic B[1][1] 3.3109
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.4908
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.8201
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.496
f_plane_restr 0.012
f_chiral_restr 0.128
f_angle_d 1.83
f_bond_d 0.019
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3941
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 432

Software

Computing
Computing Package Purpose
BLUICE Data Collection
HKL Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction