X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details 14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.36 α = 90
b = 80.2 β = 108.59
c = 54.6 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 104
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate mirrors 2013-05-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.09 14 96.5 0.08 -- -- 8.8 -- n/a -- -- 30.21
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)
2.091 2.16 91.4 0.612 -- -- 4.2 2378

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 2.091 13.84 -- 1.34 -- 49217 4922 95.52 -- 0.1929 0.1887 0.2307 --
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 2.0907 2.1144 -- 174 1216 0.3098 0.3753 -- 81.0
X Ray Diffraction 2.1144 2.1391 -- 146 1283 0.2867 0.326 -- 86.0
X Ray Diffraction 2.1391 2.1651 -- 155 1373 0.2707 0.3056 -- 87.0
X Ray Diffraction 2.1651 2.1924 -- 141 1447 0.2627 0.2834 -- 93.0
X Ray Diffraction 2.1924 2.2212 -- 167 1397 0.2725 0.3292 -- 92.0
X Ray Diffraction 2.2212 2.2515 -- 157 1515 0.2608 0.3077 -- 96.0
X Ray Diffraction 2.2515 2.2835 -- 154 1457 0.2564 0.3173 -- 94.0
X Ray Diffraction 2.2835 2.3174 -- 175 1460 0.2384 0.2602 -- 96.0
X Ray Diffraction 2.3174 2.3535 -- 203 1461 0.2279 0.2648 -- 95.0
X Ray Diffraction 2.3535 2.3919 -- 134 1483 0.2298 0.2881 -- 96.0
X Ray Diffraction 2.3919 2.4329 -- 142 1502 0.23 0.3243 -- 96.0
X Ray Diffraction 2.4329 2.4769 -- 165 1497 0.2279 0.2573 -- 97.0
X Ray Diffraction 2.4769 2.5242 -- 145 1474 0.2339 0.277 -- 96.0
X Ray Diffraction 2.5242 2.5754 -- 162 1498 0.2172 0.2692 -- 96.0
X Ray Diffraction 2.5754 2.6311 -- 173 1485 0.2177 0.2713 -- 97.0
X Ray Diffraction 2.6311 2.6918 -- 181 1528 0.2099 0.2709 -- 96.0
X Ray Diffraction 2.6918 2.7586 -- 175 1464 0.204 0.2533 -- 97.0
X Ray Diffraction 2.7586 2.8326 -- 185 1481 0.1963 0.2106 -- 97.0
X Ray Diffraction 2.8326 2.9152 -- 134 1523 0.2058 0.2586 -- 97.0
X Ray Diffraction 2.9152 3.0084 -- 147 1578 0.2032 0.2532 -- 97.0
X Ray Diffraction 3.0084 3.1147 -- 157 1449 0.197 0.2921 -- 97.0
X Ray Diffraction 3.1147 3.2379 -- 186 1547 0.1873 0.2489 -- 98.0
X Ray Diffraction 3.2379 3.3832 -- 175 1503 0.1778 0.2333 -- 98.0
X Ray Diffraction 3.3832 3.5587 -- 145 1511 0.1616 0.2004 -- 98.0
X Ray Diffraction 3.5587 3.7774 -- 172 1531 0.1644 0.1873 -- 99.0
X Ray Diffraction 3.7774 4.0622 -- 177 1510 0.1528 0.2009 -- 98.0
X Ray Diffraction 4.0622 4.4586 -- 168 1540 0.1428 0.165 -- 99.0
X Ray Diffraction 4.4586 5.0757 -- 160 1526 0.1481 0.184 -- 99.0
X Ray Diffraction 5.0757 6.2932 -- 164 1544 0.1625 0.2127 -- 99.0
X Ray Diffraction 6.2932 13.8407 -- 203 1512 0.157 0.171 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.3093
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.591
f_plane_restr 0.002
f_chiral_restr 0.038
f_angle_d 0.718
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2444
Nucleic Acid Atoms 627
Heterogen Atoms 32
Solvent Atoms 314

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.5.1 molecular replacement
SCALEPACK data reduction
DENZO data collection