X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details MPD , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.45 α = 90
b = 402.45 β = 90
c = 174.41 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-08-03
Diffraction Radiation
Monochromator Protocol
Kohzu HLD8-24 Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C

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
3.64 50 98.9 0.102 -- -- -- 157605 157605 -3.0 -3.0 111.09
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)
3.64 3.86 95.2 0.709 -- 1.84 -- --

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
FOURIER SYNTHESIS 3.64 48.335 -- 1.99 157539 157539 7889 98.89 -- 0.1582 0.1554 0.2113 FROM PDB ENTRY 2VQE
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 3.6389 3.6802 -- 212 3813 0.2835 0.3354 -- 77.0
X Ray Diffraction 3.6802 3.7235 -- 252 5014 0.2676 0.3259 -- 100.0
X Ray Diffraction 3.7235 3.7689 -- 266 4964 0.2399 0.2996 -- 100.0
X Ray Diffraction 3.7689 3.8166 -- 282 4980 0.2282 0.2857 -- 100.0
X Ray Diffraction 3.8166 3.8668 -- 284 4961 0.2183 0.2896 -- 100.0
X Ray Diffraction 3.8668 3.9197 -- 236 5005 0.2134 0.2479 -- 100.0
X Ray Diffraction 3.9197 3.9757 -- 261 5023 0.2077 0.2582 -- 100.0
X Ray Diffraction 3.9757 4.035 -- 261 4975 0.1991 0.2586 -- 100.0
X Ray Diffraction 4.035 4.0981 -- 253 5009 0.1879 0.2733 -- 100.0
X Ray Diffraction 4.0981 4.1652 -- 264 4992 0.1786 0.2574 -- 100.0
X Ray Diffraction 4.1652 4.237 -- 264 4991 0.169 0.2274 -- 100.0
X Ray Diffraction 4.237 4.314 -- 260 4991 0.1639 0.2263 -- 100.0
X Ray Diffraction 4.314 4.3969 -- 259 5018 0.1535 0.2261 -- 100.0
X Ray Diffraction 4.3969 4.4866 -- 267 5025 0.1401 0.1881 -- 100.0
X Ray Diffraction 4.4866 4.5841 -- 237 5033 0.1362 0.2017 -- 100.0
X Ray Diffraction 4.5841 4.6906 -- 262 5024 0.1385 0.2157 -- 100.0
X Ray Diffraction 4.6906 4.8078 -- 258 5008 0.1301 0.2008 -- 100.0
X Ray Diffraction 4.8078 4.9377 -- 244 5032 0.1286 0.188 -- 100.0
X Ray Diffraction 4.9377 5.0828 -- 257 5047 0.1228 0.1936 -- 100.0
X Ray Diffraction 5.0828 5.2467 -- 274 5008 0.1245 0.1662 -- 100.0
X Ray Diffraction 5.2467 5.434 -- 291 5022 0.122 0.2008 -- 100.0
X Ray Diffraction 5.434 5.6512 -- 235 5062 0.121 0.1769 -- 100.0
X Ray Diffraction 5.6512 5.908 -- 274 5044 0.1251 0.1939 -- 100.0
X Ray Diffraction 5.908 6.2189 -- 296 5031 0.1238 0.1988 -- 100.0
X Ray Diffraction 6.2189 6.6076 -- 253 5079 0.1219 0.1899 -- 100.0
X Ray Diffraction 6.6076 7.1163 -- 245 5088 0.1226 0.1681 -- 100.0
X Ray Diffraction 7.1163 7.8298 -- 264 5124 0.1294 0.1867 -- 100.0
X Ray Diffraction 7.8298 8.9565 -- 299 5044 0.1423 0.193 -- 99.0
X Ray Diffraction 8.9565 11.2607 -- 296 5102 0.1424 0.2039 -- 99.0
X Ray Diffraction 11.2607 48.3397 -- 283 5141 0.1908 0.203 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 153.943
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.382
f_plane_restr 0.008
f_chiral_restr 0.093
f_angle_d 1.915
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19093
Nucleic Acid Atoms 32507
Heterogen Atoms 295
Solvent Atoms 275

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX (phenix.refine: dev_1119) Structure Solution
PHENIX (phenix.refine: dev_1119) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction