X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.9
Temperature 298.0
Details 37% MPD, 0.1M Hepes/KOH, 10mM Phenol, 3.6mM linoleic acid, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 168.75 α = 90
b = 78.97 β = 90
c = 108.77 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-12-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.98140 BESSY 14.1

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
2.22 50 88.4 0.045 -- -- 3.05 -- 122663 -- -3.0 39.164
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)
2.22 2.32 55.6 0.187 -- 3.9 -- --

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
SAD 2.22 44.791 -- 0.87 -- 122595 6159 88.38 -- 0.2161 0.2138 0.2585 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 2.22 2.2453 -- 114 2089 0.3178 0.3656 -- 48.0
X Ray Diffraction 2.2453 2.2717 -- 130 2411 0.321 0.4089 -- 55.0
X Ray Diffraction 2.2717 2.2994 -- 142 2547 0.3047 0.4254 -- 59.0
X Ray Diffraction 2.2994 2.3285 -- 151 2858 0.3023 0.3306 -- 65.0
X Ray Diffraction 2.3285 2.3591 -- 156 3059 0.3033 0.303 -- 70.0
X Ray Diffraction 2.3591 2.3914 -- 171 3238 0.3002 0.3401 -- 74.0
X Ray Diffraction 2.3914 2.4256 -- 183 3492 0.3033 0.3601 -- 80.0
X Ray Diffraction 2.4256 2.4618 -- 190 3587 0.2922 0.3429 -- 81.0
X Ray Diffraction 2.4618 2.5003 -- 198 3720 0.2793 0.3358 -- 86.0
X Ray Diffraction 2.5003 2.5413 -- 213 3984 0.2814 0.335 -- 89.0
X Ray Diffraction 2.5413 2.5851 -- 210 3987 0.2732 0.3325 -- 91.0
X Ray Diffraction 2.5851 2.6321 -- 213 4188 0.2673 0.3154 -- 94.0
X Ray Diffraction 2.6321 2.6827 -- 220 4149 0.2642 0.3537 -- 96.0
X Ray Diffraction 2.6827 2.7374 -- 234 4320 0.2722 0.2863 -- 98.0
X Ray Diffraction 2.7374 2.797 -- 227 4315 0.254 0.2519 -- 99.0
X Ray Diffraction 2.797 2.862 -- 226 4357 0.2549 0.3209 -- 99.0
X Ray Diffraction 2.862 2.9336 -- 226 4319 0.2515 0.3239 -- 99.0
X Ray Diffraction 2.9336 3.0129 -- 233 4328 0.2467 0.3326 -- 99.0
X Ray Diffraction 3.0129 3.1015 -- 229 4270 0.2422 0.3013 -- 98.0
X Ray Diffraction 3.1015 3.2016 -- 228 4325 0.2257 0.2698 -- 98.0
X Ray Diffraction 3.2016 3.316 -- 234 4309 0.2173 0.2927 -- 98.0
X Ray Diffraction 3.316 3.4487 -- 229 4360 0.2122 0.2329 -- 98.0
X Ray Diffraction 3.4487 3.6056 -- 230 4282 0.1901 0.235 -- 98.0
X Ray Diffraction 3.6056 3.7956 -- 227 4274 0.187 0.2378 -- 98.0
X Ray Diffraction 3.7956 4.0333 -- 226 4314 0.1716 0.1919 -- 98.0
X Ray Diffraction 4.0333 4.3444 -- 227 4320 0.1592 0.1981 -- 98.0
X Ray Diffraction 4.3444 4.7812 -- 228 4280 0.1563 0.2166 -- 98.0
X Ray Diffraction 4.7812 5.472 -- 220 4273 0.1672 0.2126 -- 97.0
X Ray Diffraction 5.472 6.8901 -- 229 4250 0.1869 0.2012 -- 97.0
X Ray Diffraction 6.8901 44.7999 -- 215 4231 0.1792 0.2066 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 64.7363
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.185
f_plane_restr 0.006
f_chiral_restr 0.08
f_angle_d 1.194
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9367
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 473

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHELXD Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SHELX phasing
Xscale data reduction