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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: 30mg/ml R699, 2mM MnCl2.
mother liquor: 0.2 M Ammonium formate, 20% (w/v) PEG 3350
The ratio of mix and mother liquor was at 1:1.
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.821 α = 90 b = 121.696 β = 118.589 c = 72.69 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 2022-12-13 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 1.8 61.383 98.8 0.079 0.998 10.7 6.8 97211
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 1.8 1.83 99.3 0.908 0.864 1.7 6.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 61.383 97161 4915 98.669 0.191 0.1895 0.2199 0.2317 33.623
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] 0.213 -0.825 3.899 -2.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.976 r_dihedral_angle_3_deg 12.821 r_lrange_it 6.925 r_dihedral_angle_1_deg 6.752 r_scangle_it 5.565 r_dihedral_angle_2_deg 5.096 r_mcangle_it 3.834 r_scbond_it 3.695 r_mcbond_it 2.724 r_angle_refined_deg 1.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.976 r_dihedral_angle_3_deg 12.821 r_lrange_it 6.925 r_dihedral_angle_1_deg 6.752 r_scangle_it 5.565 r_dihedral_angle_2_deg 5.096 r_mcangle_it 3.834 r_scbond_it 3.695 r_mcbond_it 2.724 r_angle_refined_deg 1.536 r_nbtor_refined 0.317 r_symmetry_nbd_refined 0.213 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.129 r_chiral_restr 0.108 r_ncsr_local_group_1 0.094 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7220 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 2
Software Software Software Name Purpose DIALS data collection xia2 data reduction Aimless data scaling PHENIX phasing PHASER phasing Coot model building REFMAC refinement