NEUTRON DIFFRACTION - X-RAY DIFFRACTION Experimental Data & Validation


Structure 6GCY has been solved using multiple methods: NEUTRON DIFFRACTION - X-RAY DIFFRACTION

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 1.2 M sodium citrate, 0.1 M Tris pH 8.5 in Hampton sandwich box set-ups. Drops were 150-250 uL and we set-up in a 1:1 ratio. To get the complex with SGC ligand we did "dry co-crystallization".

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.61 α = 90
b = 41.94 β = 104.01
c = 72.77 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
2 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2016-12-15
IMAGE PLATE MAATEL IMAGINE -- 2018-03-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM30A 1.04 ESRF BM30A
NUCLEAR REACTOR FRM II BEAMLINE BIODIFF 2.66 FRM II BIODIFF

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
2 50 93.0 0.168 -- -- 2.3 -- 16153 -- -- --
1.3 36 97.6 0.051 -- -- 7.3 -- 60056 -- -- --
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)
1.3 1.4 -- 0.524 -- -- -- --

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 2.0 29.009 -- 1.5 -- 16142 1603 92.95 -- 0.1931 0.191 0.2122 --
MOLECULAR REPLACEMENT 1.3 20.97 -- 1.37 -- 60047 3601 97.62 -- 0.1484 0.1478 0.1551 --
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)
Neutron Diffraction 1.9895 2.0537 -- 90 887 0.2704 0.2973 -- 63.0
Neutron Diffraction 2.0537 2.1271 -- 152 1316 0.2569 0.2781 -- 93.0
Neutron Diffraction 2.1271 2.2122 -- 148 1368 0.2452 0.2915 -- 96.0
Neutron Diffraction 2.2122 2.3129 -- 132 1307 0.2402 0.2706 -- 92.0
Neutron Diffraction 2.3129 2.4347 -- 148 1307 0.2147 0.2472 -- 94.0
Neutron Diffraction 2.4347 2.5872 -- 156 1394 0.1949 0.1974 -- 98.0
Neutron Diffraction 2.5872 2.7868 -- 155 1381 0.1908 0.1929 -- 97.0
Neutron Diffraction 2.7868 3.067 -- 147 1389 0.1728 0.2157 -- 98.0
Neutron Diffraction 3.067 3.5101 -- 158 1388 0.1574 0.1877 -- 97.0
Neutron Diffraction 3.5101 4.4199 -- 155 1383 0.1356 0.1533 -- 97.0
Neutron Diffraction 4.4199 29.0123 -- 162 1419 0.1467 0.153 -- 96.0
X Ray Diffraction 1.3 1.3171 -- 89 2060 0.2193 0.2382 -- 92.0
X Ray Diffraction 1.3171 1.3351 -- 109 2128 0.1956 0.2226 -- 96.0
X Ray Diffraction 1.3351 1.3542 -- 113 2179 0.1925 0.2062 -- 97.0
X Ray Diffraction 1.3542 1.3744 -- 100 2152 0.1971 0.1995 -- 95.0
X Ray Diffraction 1.3744 1.3959 -- 99 2190 0.1921 0.2188 -- 97.0
X Ray Diffraction 1.3959 1.4188 -- 100 2163 0.1881 0.185 -- 96.0
X Ray Diffraction 1.4188 1.4432 -- 107 2167 0.1845 0.1861 -- 98.0
X Ray Diffraction 1.4432 1.4695 -- 92 2170 0.18 0.2257 -- 96.0
X Ray Diffraction 1.4695 1.4977 -- 111 2219 0.1787 0.1897 -- 98.0
X Ray Diffraction 1.4977 1.5283 -- 119 2143 0.175 0.2063 -- 96.0
X Ray Diffraction 1.5283 1.5615 -- 88 2225 0.1743 0.1997 -- 98.0
X Ray Diffraction 1.5615 1.5978 -- 117 2146 0.1647 0.2132 -- 97.0
X Ray Diffraction 1.5978 1.6378 -- 99 2204 0.1677 0.1889 -- 97.0
X Ray Diffraction 1.6378 1.682 -- 106 2240 0.1722 0.1881 -- 99.0
X Ray Diffraction 1.682 1.7315 -- 110 2167 0.1681 0.1804 -- 98.0
X Ray Diffraction 1.7315 1.7874 -- 107 2229 0.1662 0.1935 -- 98.0
X Ray Diffraction 1.7874 1.8512 -- 108 2215 0.1617 0.1667 -- 98.0
X Ray Diffraction 1.8512 1.9253 -- 107 2240 0.1537 0.1507 -- 99.0
X Ray Diffraction 1.9253 2.0128 -- 116 2206 0.1484 0.1715 -- 99.0
X Ray Diffraction 2.0128 2.1189 -- 211 2138 0.1471 0.1693 -- 99.0
X Ray Diffraction 2.1189 2.2515 -- 229 2110 0.146 0.1507 -- 99.0
X Ray Diffraction 2.2515 2.4251 -- 212 2144 0.1443 0.1431 -- 99.0
X Ray Diffraction 2.4251 2.6687 -- 241 2135 0.139 0.1554 -- 99.0
X Ray Diffraction 2.6687 3.0538 -- 229 2153 0.1364 0.1619 -- 99.0
X Ray Diffraction 3.0538 3.8436 -- 239 2147 0.1198 0.1421 -- 100.0
X Ray Diffraction 3.8436 20.9727 -- 243 2176 0.1123 0.122 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_dihedral_angle_d 19.992
f_chiral_restr 0.092
f_plane_restr 0.006
f_bond_d 0.009
f_bond_d 0.009
f_angle_d 1.173
f_chiral_restr 0.092
f_angle_d 1.173
f_dihedral_angle_d 19.992
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2052
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 209

Software

Software
Software Name Purpose
PHENIX refinement version: (1.12_2829: ???)
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing