☰ Navigation Tabs
X-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoeba polyphaga Minivirus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 13-16% PEG-5000, 2% ethylene glycol, 100 mM HEPES, in the presence of 5 mM dTDP
Crystal Properties Matthews coefficient Solvent content 2.34 47.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.883 α = 90 b = 111.083 β = 90 c = 133.385 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97918 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.05 50 99.5 0.086 44.5 8.3 87647
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 98.4 0.298 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1R66 2.05 38.88 83130 4517 99.24 0.183 0.1805 0.1891 0.2291 0.2333 RANDOM 33.577
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.06 0.6 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.6 r_dihedral_angle_3_deg 16.013 r_dihedral_angle_4_deg 13.021 r_dihedral_angle_1_deg 7.101 r_angle_refined_deg 1.559 r_angle_other_deg 1.337 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.6 r_dihedral_angle_3_deg 16.013 r_dihedral_angle_4_deg 13.021 r_dihedral_angle_1_deg 7.101 r_angle_refined_deg 1.559 r_angle_other_deg 1.337 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10133 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 245
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing