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Acanthamoeba Polyphaga Mimivirus R699
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other other solved exp. R699 model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Protein/cofactor mix: 12mg/ml R699, 10mM MnCl2, 10mM UDP glucose, 50% glycerol.
Mother liquor: 0.18 M Ammonium chloride, 18% (w/v) PEG 3350, 4% v/v 1-Propanol.
The ratio of mix and mother liquor was at 1:1.
Crystal Properties Matthews coefficient Solvent content 2.4 48.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.041 α = 90 b = 71.481 β = 123.178 c = 72.626 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS EIGER X 16M 2022-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.75 60.79 99.3 0.083 0.998 10.9 6.9 349711
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 98.5 0.491 0.921 2.7 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.75 57.98 50656 2462 99.166 0.172 0.1706 0.1789 0.1953 0.2051 20.727
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] 3.44 -1.188 -0.387 -0.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.805 r_dihedral_angle_3_deg 12.17 r_dihedral_angle_1_deg 6.877 r_lrange_it 6.216 r_dihedral_angle_2_deg 6.079 r_scangle_it 4.593 r_mcangle_it 2.979 r_scbond_it 2.883 r_mcbond_it 1.892 r_angle_refined_deg 1.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.805 r_dihedral_angle_3_deg 12.17 r_dihedral_angle_1_deg 6.877 r_lrange_it 6.216 r_dihedral_angle_2_deg 6.079 r_scangle_it 4.593 r_mcangle_it 2.979 r_scbond_it 2.883 r_mcbond_it 1.892 r_angle_refined_deg 1.695 r_nbtor_refined 0.318 r_nbd_refined 0.201 r_symmetry_nbd_refined 0.194 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.149 r_chiral_restr 0.119 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3605 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 38
Software Software Software Name Purpose DIALS data collection xia2 data reduction Aimless data scaling PHENIX phasing PHASER phasing Coot model building REFMAC refinement