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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/substrate/cofactor mix: 28 mg/ml R699, 10 mM UDP glucose, 10 mM MnCl2, 0.15 g/ml glucose, 0.15 g/ml galactose.
Mother liquor: 0.1 M HEPES pH 7, 10% (w/v) PEG 6000.
The ratio of mix and mother liquor was at 1:1.
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.153 α = 90 b = 124.998 β = 118.295 c = 72.757 γ = 90
Symmetry Space Group P 1 21 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 2023-02-28 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 1.5 62.5 98.4 0.059 0.998 13.3 6.8 171464
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 1.5 1.52 0.602 0.857 1.8 6.3
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 1.5 60.965 171272 8633 98.733 0.167 0.1657 0.1674 0.189 0.1911 20.922
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] 0.197 -0.376 1.682 -0.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.906 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_1_deg 6.762 r_lrange_it 5.881 r_dihedral_angle_2_deg 5.853 r_lrange_other 5.806 r_scangle_it 4.697 r_scangle_other 4.696 r_scbond_it 3.103 r_scbond_other 3.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.906 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_1_deg 6.762 r_lrange_it 5.881 r_dihedral_angle_2_deg 5.853 r_lrange_other 5.806 r_scangle_it 4.697 r_scangle_other 4.696 r_scbond_it 3.103 r_scbond_other 3.102 r_mcangle_it 2.665 r_mcangle_other 2.665 r_mcbond_it 1.844 r_mcbond_other 1.842 r_angle_refined_deg 1.8 r_angle_other_deg 0.624 r_nbd_refined 0.223 r_nbtor_refined 0.181 r_symmetry_nbd_other 0.176 r_symmetry_nbd_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.168 r_nbd_other 0.146 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.098 r_ncsr_local_group_1 0.091 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7306 Nucleic Acid Atoms Solvent Atoms 883 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement DIALS data collection xia2 data reduction Aimless data scaling PHENIX phasing PHASER phasing Coot model building