X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 291.0
Details 14.55% PEG-4000, 0.2M ammonium acetate, 0.1M sodium citrate, 1:100 (w/w) chymotrypsin and 0.005M ADP., pH 6.0, vapor diffusion, sitting drop, temperature 291K
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 291.0
Details 15% PEG-4000, 0.2M ammonium acetate, 0.1M sodium citrate, 1:100 (w/w) chymotrypsin and 0.005M ADP., pH 5.6, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.95 α = 90
b = 127.95 β = 90
c = 127.25 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2007-11-29
CCD ADSC QUANTUM 315 -- 2008-04-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.97926 APS 23-ID-B
SYNCHROTRON APS BEAMLINE 19-ID 0.97921 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
2.84 30 100.0 0.089 -- -- 11.1 -- 29072 -- -- --
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)
2.84 2.94 100.0 0.978 -- -- 10.5 2860

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 2.84 30.0 -- 0.0 -- 28742 1071 99.653 -- 0.207 0.205 0.245 THIN SHELLS (SFTOOLS)
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 2.84 2.913 -- 0 2092 0.382 -- -- 98.819
X Ray Diffraction 2.913 2.992 -- 0 2003 0.32 -- -- 99.06
X Ray Diffraction 2.992 3.078 -- 188 1766 0.288 0.367 -- 99.491
X Ray Diffraction 3.078 3.172 -- 0 1924 0.268 -- -- 99.329
X Ray Diffraction 3.172 3.274 -- 157 1726 0.257 0.298 -- 99.735
X Ray Diffraction 3.274 3.388 -- 0 1782 0.253 -- -- 99.442
X Ray Diffraction 3.388 3.514 -- 151 1597 0.226 0.286 -- 99.772
X Ray Diffraction 3.514 3.656 -- 0 1698 0.208 -- -- 99.706
X Ray Diffraction 3.656 3.815 -- 136 1470 0.2 0.253 -- 99.752
X Ray Diffraction 3.815 3.998 -- 0 1554 0.186 -- -- 99.743
X Ray Diffraction 3.998 4.211 -- 114 1357 0.173 0.205 -- 100.0
X Ray Diffraction 4.211 4.461 -- 84 1325 0.173 0.185 -- 100.0
X Ray Diffraction 4.461 4.761 -- 0 1346 0.149 -- -- 100.0
X Ray Diffraction 4.761 5.132 -- 65 1165 0.175 0.176 -- 100.0
X Ray Diffraction 5.132 5.605 -- 51 1105 0.204 0.329 -- 100.0
X Ray Diffraction 5.605 6.24 -- 15 1038 0.232 0.419 -- 100.0
X Ray Diffraction 6.24 7.153 -- 19 917 0.21 0.233 -- 100.0
X Ray Diffraction 7.153 8.639 -- 47 765 0.159 0.214 -- 100.0
X Ray Diffraction 8.639 11.741 -- 25 627 0.147 0.159 -- 100.0
X Ray Diffraction 11.741 30.0 -- 19 414 0.226 0.357 -- 99.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.804
Anisotropic B[1][1] 0.212
Anisotropic B[1][2] 0.106
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.212
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.317
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.868
r_scangle_it 1.559
r_angle_refined_deg 1.131
r_dihedral_angle_3_deg 12.927
r_mcangle_it 1.452
r_bond_other_d 0.002
r_dihedral_angle_4_deg 15.853
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 35.173
r_scbond_it 0.942
r_mcbond_it 0.818
r_dihedral_angle_1_deg 4.387
r_chiral_restr 0.063
r_gen_planes_refined 0.004
r_bond_refined_d 0.012
r_mcbond_other 0.114
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5885
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.11
REFMAC refinement version: 5.5.0044
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data scaling