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_angle_d 1.915
f_chiral_restr 0.093
f_bond_d 0.013
f_dihedral_angle_d 20.382
f_plane_restr 0.008
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

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: dev_1119
PDB_EXTRACT data extraction version: 3.11
ADSC data collection version: Quantum
PHENIX phasing version: dev_1119