X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 289.0
Details 1.6 M Na-Acetate, 0.1 M Na-Citrate, pH 6.5, vapor diffusion, hanging drop, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.12 α = 90
b = 68.72 β = 90
c = 89.89 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
-- -- -- 2011-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
1.4 50 96.5 0.052 -- -- 4.3 77799 73877 -- -- --
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)
1.4 1.42 94.5 -- -- -- 4.1 --

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 1.4 41.01 -- 1.34 -- 73824 7379 96.3 -- 0.178 0.175 0.198 --
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 1.4 1.4143 -- 218 1986 0.3712 0.3757 -- 87.0
X Ray Diffraction 1.4143 1.431 -- 234 2145 0.3599 0.3865 -- 94.0
X Ray Diffraction 1.431 1.4484 -- 242 2160 0.3285 0.3097 -- 94.0
X Ray Diffraction 1.4484 1.4668 -- 239 2136 0.2976 0.3412 -- 95.0
X Ray Diffraction 1.4668 1.4861 -- 241 2143 0.2743 0.2794 -- 95.0
X Ray Diffraction 1.4861 1.5064 -- 242 2147 0.2555 0.2315 -- 95.0
X Ray Diffraction 1.5064 1.5279 -- 241 2193 0.2427 0.2357 -- 95.0
X Ray Diffraction 1.5279 1.5507 -- 229 2171 0.2193 0.2737 -- 95.0
X Ray Diffraction 1.5507 1.575 -- 249 2167 0.2185 0.1871 -- 96.0
X Ray Diffraction 1.575 1.6008 -- 247 2185 0.2081 0.243 -- 96.0
X Ray Diffraction 1.6008 1.6284 -- 237 2191 0.1895 0.2333 -- 96.0
X Ray Diffraction 1.6284 1.658 -- 247 2191 0.1796 0.1925 -- 96.0
X Ray Diffraction 1.658 1.6899 -- 243 2192 0.176 0.1903 -- 96.0
X Ray Diffraction 1.6899 1.7244 -- 245 2199 0.1769 0.1963 -- 96.0
X Ray Diffraction 1.7244 1.7619 -- 247 2229 0.1733 0.2115 -- 97.0
X Ray Diffraction 1.7619 1.8029 -- 246 2180 0.175 0.204 -- 97.0
X Ray Diffraction 1.8029 1.848 -- 253 2257 0.1734 0.1937 -- 97.0
X Ray Diffraction 1.848 1.8979 -- 245 2200 0.1671 0.1808 -- 97.0
X Ray Diffraction 1.8979 1.9538 -- 252 2252 0.1665 0.1788 -- 97.0
X Ray Diffraction 1.9538 2.0168 -- 250 2233 0.1669 0.181 -- 98.0
X Ray Diffraction 2.0168 2.0889 -- 246 2246 0.1606 0.1728 -- 98.0
X Ray Diffraction 2.0889 2.1726 -- 247 2240 0.1614 0.1915 -- 98.0
X Ray Diffraction 2.1726 2.2714 -- 252 2283 0.1529 0.1711 -- 98.0
X Ray Diffraction 2.2714 2.3912 -- 251 2266 0.1484 0.1652 -- 98.0
X Ray Diffraction 2.3912 2.541 -- 253 2286 0.1569 0.178 -- 99.0
X Ray Diffraction 2.541 2.7371 -- 251 2299 0.1626 0.2032 -- 99.0
X Ray Diffraction 2.7371 3.0125 -- 257 2297 0.1787 0.1983 -- 99.0
X Ray Diffraction 3.0125 3.4482 -- 258 2325 0.1675 0.1861 -- 98.0
X Ray Diffraction 3.4482 4.3436 -- 256 2305 0.1536 0.1675 -- 97.0
X Ray Diffraction 4.3436 41.0262 -- 261 2341 0.1936 0.2359 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.13
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.131
f_dihedral_angle_d 14.639
f_angle_d 1.001
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2577
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 339

Software

Computing
Computing Package Purpose
SCALEPACK Data Reduction (data scaling)
PHENIX (PHENIX.REFINE: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALEPACK data reduction