X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.13 α = 90
b = 402.13 β = 90
c = 172.61 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 -- 2010-11-07
Diffraction Radiation
Monochromator Protocol
Kohzu HLD8-24 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
3.68 35 98.3 0.102 -- -- 2.9 149012 149012 -3.0 -3.0 --
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)
3.683 3.83 98.5 0.608 -- -- 2.7 14757

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 3.683 34.555 -- 1.34 148962 148962 7392 98.14 -- 0.1586 0.1558 0.2115 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 3.683 3.7249 -- 224 4453 0.2741 0.3282 -- 94.0
X Ray Diffraction 3.7249 3.7686 -- 272 4678 0.248 0.3026 -- 98.0
X Ray Diffraction 3.7686 3.8145 -- 205 4727 0.2449 0.3277 -- 99.0
X Ray Diffraction 3.8145 3.8628 -- 257 4708 0.2302 0.289 -- 99.0
X Ray Diffraction 3.8628 3.9135 -- 247 4757 0.2227 0.2696 -- 100.0
X Ray Diffraction 3.9135 3.9671 -- 237 4723 0.2129 0.259 -- 100.0
X Ray Diffraction 3.9671 4.0237 -- 273 4740 0.2168 0.281 -- 100.0
X Ray Diffraction 4.0237 4.0836 -- 274 4705 0.2029 0.2583 -- 100.0
X Ray Diffraction 4.0836 4.1473 -- 240 4738 0.1835 0.2352 -- 99.0
X Ray Diffraction 4.1473 4.2152 -- 245 4771 0.1728 0.262 -- 100.0
X Ray Diffraction 4.2152 4.2878 -- 240 4739 0.173 0.2262 -- 99.0
X Ray Diffraction 4.2878 4.3656 -- 267 4718 0.1676 0.2386 -- 99.0
X Ray Diffraction 4.3656 4.4494 -- 267 4731 0.1603 0.2137 -- 100.0
X Ray Diffraction 4.4494 4.54 -- 262 4731 0.1538 0.2224 -- 99.0
X Ray Diffraction 4.54 4.6385 -- 235 4743 0.1446 0.1915 -- 99.0
X Ray Diffraction 4.6385 4.7461 -- 225 4767 0.1397 0.2195 -- 99.0
X Ray Diffraction 4.7461 4.8645 -- 243 4781 0.1366 0.1958 -- 99.0
X Ray Diffraction 4.8645 4.9957 -- 264 4714 0.1314 0.2018 -- 99.0
X Ray Diffraction 4.9957 5.1422 -- 225 4781 0.1295 0.2099 -- 99.0
X Ray Diffraction 5.1422 5.3076 -- 246 4723 0.1268 0.1976 -- 99.0
X Ray Diffraction 5.3076 5.4966 -- 253 4752 0.1183 0.1752 -- 99.0
X Ray Diffraction 5.4966 5.7157 -- 247 4731 0.1178 0.2038 -- 98.0
X Ray Diffraction 5.7157 5.9746 -- 228 4753 0.1237 0.1659 -- 98.0
X Ray Diffraction 5.9746 6.2878 -- 226 4738 0.1217 0.1892 -- 98.0
X Ray Diffraction 6.2878 6.6791 -- 251 4735 0.1194 0.1733 -- 98.0
X Ray Diffraction 6.6791 7.1905 -- 243 4721 0.1162 0.1703 -- 97.0
X Ray Diffraction 7.1905 7.9063 -- 229 4697 0.1164 0.1818 -- 96.0
X Ray Diffraction 7.9063 9.0325 -- 270 4633 0.1195 0.1588 -- 95.0
X Ray Diffraction 9.0325 11.3133 -- 239 4740 0.1352 0.1792 -- 96.0
X Ray Diffraction 11.3133 34.5564 -- 258 4642 0.2114 0.237 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 148.635
Anisotropic B[1][1] -14.4644
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -14.4644
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 22.2271
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.674
f_plane_restr 0.01
f_chiral_restr 0.099
f_angle_d 1.821
f_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32508
Heterogen Atoms 315
Solvent Atoms 389

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: dev_978) Structure Solution
PHENIX (phenix.refine: dev_978) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection