X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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_angle_d 0.718
f_chiral_restr 0.038
f_bond_d 0.003
f_dihedral_angle_d 18.591
f_plane_restr 0.002
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

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.5.1
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11