X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 289.0
Details 0.09M malonic acid, 0.0125M ammonium citratic tribasic, 0.006M succinic acid, 0.015M DL-malic acid, 0.01M sodium acetate, 0.025M sodium formate, 0.008M ammonium tartrate, 0.1M HEPES:NaOH, 10% (w/v) PEG MME 5000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.94 α = 90
b = 129.19 β = 90
c = 165.12 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 ADSC QUANTUM 315r mirror 2013-10-09
Diffraction Radiation
Monochromator Protocol
Si 111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97938 APS 19-ID

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
2.12 41 99.9 0.081 -- -- 6.0 153814 153814 0.0 -5.0 35.14
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)
2.12 2.16 100.0 0.685 -- 2.64 5.9 7594

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 2.12 40.78 -- 1.33 153197 153197 7692 99.48 -- 0.1648 0.163 0.1981 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 2.12 2.1434 -- 231 4697 0.2374 0.2797 -- 97.0
X Ray Diffraction 2.1434 2.1686 -- 270 4812 0.2216 0.2734 -- 100.0
X Ray Diffraction 2.1686 2.195 -- 250 4833 0.2114 0.2466 -- 100.0
X Ray Diffraction 2.195 2.2228 -- 234 4837 0.2116 0.2689 -- 100.0
X Ray Diffraction 2.2228 2.2521 -- 257 4791 0.2061 0.2734 -- 100.0
X Ray Diffraction 2.2521 2.2829 -- 247 4844 0.2053 0.259 -- 100.0
X Ray Diffraction 2.2829 2.3155 -- 263 4830 0.2023 0.2586 -- 100.0
X Ray Diffraction 2.3155 2.3501 -- 258 4812 0.2002 0.2515 -- 100.0
X Ray Diffraction 2.3501 2.3868 -- 240 4845 0.1962 0.2616 -- 100.0
X Ray Diffraction 2.3868 2.4259 -- 250 4787 0.1875 0.2318 -- 100.0
X Ray Diffraction 2.4259 2.4678 -- 266 4799 0.1823 0.2421 -- 100.0
X Ray Diffraction 2.4678 2.5126 -- 236 4863 0.1834 0.2418 -- 100.0
X Ray Diffraction 2.5126 2.561 -- 263 4807 0.1758 0.2497 -- 99.0
X Ray Diffraction 2.561 2.6132 -- 241 4859 0.1758 0.2009 -- 99.0
X Ray Diffraction 2.6132 2.67 -- 274 4801 0.1812 0.23 -- 100.0
X Ray Diffraction 2.67 2.7321 -- 249 4811 0.1828 0.2572 -- 99.0
X Ray Diffraction 2.7321 2.8004 -- 275 4803 0.1791 0.2149 -- 99.0
X Ray Diffraction 2.8004 2.8761 -- 262 4877 0.1824 0.2456 -- 100.0
X Ray Diffraction 2.8761 2.9607 -- 243 4818 0.1814 0.2216 -- 99.0
X Ray Diffraction 2.9607 3.0563 -- 281 4804 0.1801 0.2 -- 99.0
X Ray Diffraction 3.0563 3.1655 -- 270 4857 0.1873 0.2489 -- 100.0
X Ray Diffraction 3.1655 3.2922 -- 259 4847 0.178 0.2276 -- 100.0
X Ray Diffraction 3.2922 3.4419 -- 252 4873 0.1699 0.2179 -- 100.0
X Ray Diffraction 3.4419 3.6233 -- 252 4887 0.1587 0.1916 -- 100.0
X Ray Diffraction 3.6233 3.8501 -- 272 4869 0.1465 0.1645 -- 100.0
X Ray Diffraction 3.8501 4.1471 -- 259 4893 0.1396 0.162 -- 100.0
X Ray Diffraction 4.1471 4.564 -- 244 4922 0.1205 0.1454 -- 100.0
X Ray Diffraction 4.564 5.2232 -- 258 4968 0.1263 0.1549 -- 100.0
X Ray Diffraction 5.2232 6.5763 -- 270 4994 0.1491 0.1768 -- 100.0
X Ray Diffraction 6.5763 40.7878 -- 266 5065 0.1547 0.1591 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.07
f_angle_d 1.053
f_bond_d 0.007
f_plane_restr 0.005
f_dihedral_angle_d 14.338
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16085
Nucleic Acid Atoms 0
Heterogen Atoms 124
Solvent Atoms 900

Software

Software
Software Name Purpose
SBC-Collect data collection
SHELXD phasing
MLPHARE phasing
DM model building
ARP model building
WARP model building
HKL-3000 phasing
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
HKL-3000 data reduction
HKL-3000 data scaling
DM phasing