X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 298.0
Details 27 mg/mL protein in 1.3M (NH4)2SO4, 0.05M NaH2P2O7, 3% ethylene glycol. Not streak-seeded, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.19 α = 90
b = 46.43 β = 128.84
c = 62.87 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 Si(111) monochromator with sagittally bent second crystal 2009-08-12
Diffraction Radiation
Monochromator Protocol
Si111 - sagittal second crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.8 32.5 88.3 0.0707 0.0707 -- 3.3 -- 20497 0.0 0.0 41.13
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)
1.8 1.864 47.8 0.4537 0.4537 1.69 1.67 --

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 1.72 31.123 -- 0.0 -- 20333 1984 99.2 -- 0.1756 0.1723 0.206 --
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 1.7198 1.7628 -- 143 1260 0.2542 0.3249 -- 97.0
X Ray Diffraction 1.7628 1.8105 -- 135 1322 0.2356 0.2831 -- 98.0
X Ray Diffraction 1.8105 1.8638 -- 138 1279 0.2341 0.2486 -- 98.0
X Ray Diffraction 1.8638 1.9239 -- 138 1262 0.2036 0.2619 -- 99.0
X Ray Diffraction 1.9239 1.9927 -- 148 1304 0.1917 0.201 -- 99.0
X Ray Diffraction 1.9927 2.0724 -- 135 1298 0.175 0.2194 -- 99.0
X Ray Diffraction 2.0724 2.1667 -- 144 1332 0.1614 0.2113 -- 100.0
X Ray Diffraction 2.1667 2.2809 -- 142 1300 0.1457 0.1767 -- 100.0
X Ray Diffraction 2.2809 2.4238 -- 141 1319 0.1431 0.1712 -- 100.0
X Ray Diffraction 2.4238 2.6108 -- 137 1325 0.1485 0.1831 -- 100.0
X Ray Diffraction 2.6108 2.8734 -- 149 1318 0.1495 0.183 -- 100.0
X Ray Diffraction 2.8734 3.2888 -- 144 1328 0.1725 0.2087 -- 100.0
X Ray Diffraction 3.2888 4.142 -- 139 1330 0.1631 0.1879 -- 100.0
X Ray Diffraction 4.142 31.1278 -- 151 1372 0.1826 0.2137 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.1251
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.481
f_bond_d 0.018
f_chiral_restr 0.056
f_plane_restr 0.009
f_dihedral_angle_d 16.956
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1103
Nucleic Acid Atoms 0
Heterogen Atoms 91
Solvent Atoms 114

Software

Software
Software Name Purpose
PHENIX refinement version: 1.8_1069
PHASER phasing
REFMAC refinement version: 5.5.0109
X-GEN data reduction
X-GEN data scaling
SERGUI data collection