X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 289.0
Details 0.2 M ammonium sulphate, 0.1 M Bis-Tris pH 5.5, 25 %(w/v) PEG 3350, 100 mM ampicillin, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.19 α = 90
b = 79.17 β = 90
c = 134.47 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 mirrors 2011-08-15
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.5166 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
1.05 50 94.9 -- 0.089 -- 5.5 185255 185255 0.0 0.0 7.76
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)
1.05 1.06 88.9 -- 0.023 0.871 5.7 5746

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 1.05 17.561 -- 0.0 184744 184744 9286 94.65 0.134 0.134 0.133 0.157 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 1.0503 1.0623 5646 288 5358 0.2106 0.2496 -- 87.0
X Ray Diffraction 1.0623 1.0748 5723 275 5448 0.1918 0.2151 -- 90.0
X Ray Diffraction 1.0748 1.0879 5787 274 5513 0.1817 0.2035 -- 89.0
X Ray Diffraction 1.0879 1.1017 5775 300 5475 0.1705 0.1946 -- 90.0
X Ray Diffraction 1.1017 1.1161 5823 318 5505 0.1569 0.1787 -- 90.0
X Ray Diffraction 1.1161 1.1314 5797 280 5517 0.1499 0.1609 -- 90.0
X Ray Diffraction 1.1314 1.1476 5829 312 5517 0.1507 0.1712 -- 90.0
X Ray Diffraction 1.1476 1.1647 5859 296 5563 0.1471 0.1591 -- 91.0
X Ray Diffraction 1.1647 1.1829 5896 286 5610 0.1388 0.1743 -- 91.0
X Ray Diffraction 1.1829 1.2023 5881 282 5599 0.1421 0.1692 -- 92.0
X Ray Diffraction 1.2023 1.223 5943 290 5653 0.1363 0.1697 -- 92.0
X Ray Diffraction 1.223 1.2453 6013 295 5718 0.135 0.1678 -- 93.0
X Ray Diffraction 1.2453 1.2692 6045 332 5713 0.1307 0.1609 -- 93.0
X Ray Diffraction 1.2692 1.2951 6077 312 5765 0.1254 0.1597 -- 94.0
X Ray Diffraction 1.2951 1.3233 6098 292 5806 0.1233 0.1445 -- 94.0
X Ray Diffraction 1.3233 1.354 6189 317 5872 0.1262 0.1463 -- 95.0
X Ray Diffraction 1.354 1.3879 6212 336 5876 0.12 0.1507 -- 96.0
X Ray Diffraction 1.3879 1.4254 6236 342 5896 0.1129 0.1495 -- 96.0
X Ray Diffraction 1.4254 1.4673 6345 324 6021 0.1088 0.1344 -- 98.0
X Ray Diffraction 1.4673 1.5146 6350 320 6030 0.1103 0.143 -- 98.0
X Ray Diffraction 1.5146 1.5688 6419 328 6091 0.1028 0.1348 -- 98.0
X Ray Diffraction 1.5688 1.6315 6459 301 6158 0.1055 0.1269 -- 99.0
X Ray Diffraction 1.6315 1.7057 6465 296 6169 0.1059 0.1319 -- 99.0
X Ray Diffraction 1.7057 1.7956 6512 322 6190 0.114 0.1265 -- 100.0
X Ray Diffraction 1.7956 1.9079 6486 328 6158 0.1181 0.1381 -- 100.0
X Ray Diffraction 1.9079 2.055 6607 352 6255 0.1174 0.1458 -- 100.0
X Ray Diffraction 2.055 2.2615 6575 312 6263 0.1212 0.1403 -- 100.0
X Ray Diffraction 2.2615 2.5878 6619 304 6315 0.1332 0.1555 -- 100.0
X Ray Diffraction 2.5878 3.257 6687 340 6347 0.1417 0.1596 -- 100.0
X Ray Diffraction 3.257 17.5637 6389 332 6057 0.1566 0.1839 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.8
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.011
f_chiral_restr 0.121
f_dihedral_angle_d 13.824
f_angle_d 1.808
f_bond_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3609
Nucleic Acid Atoms 0
Heterogen Atoms 83
Solvent Atoms 612

Software

Computing
Computing Package Purpose
SBCCOLLECT, HKL3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL3000, Molrep Structure Solution
SHelx, PHENIX (phenix.refine: 1.8.1_1161) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1161) refinement
SHelx refinement
Molrep model building
HKL3000 model building
HKL3000 data collection
SBCCOLLECT data collection