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Acanthamoeba Polyphaga Mimivirus L230
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein/cofactor mix: 15mg/ml L230, 500uM FeCl2
Mother Liquor: 0.04 M potassium dihydrogen phosphate, 16 % w/v PEG 8000, 20 % v/v Glycerol
The ratio of mix and mother liquor was at 1:1.
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.61 α = 90 b = 109.61 β = 90 c = 84.954 γ = 90
Symmetry Space Group P 43 21 2
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 2021-04-05 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 2.3 49.02 100 0.16 0.999 15.7 25.7 23603
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 2.3 2.38 100 1.002 0.936 4.2 27.1
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 2.3 49.015 23546 1210 99.877 0.207 0.2047 0.2047 0.2509 0.2511 33.423
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] -0.116 -0.116 0.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.623 r_dihedral_angle_3_deg 12.852 r_lrange_it 7.707 r_dihedral_angle_1_deg 7.354 r_dihedral_angle_2_deg 6.809 r_scangle_it 6.194 r_mcangle_it 4.217 r_scbond_it 4.064 r_mcbond_it 2.748 r_angle_refined_deg 1.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.623 r_dihedral_angle_3_deg 12.852 r_lrange_it 7.707 r_dihedral_angle_1_deg 7.354 r_dihedral_angle_2_deg 6.809 r_scangle_it 6.194 r_mcangle_it 4.217 r_scbond_it 4.064 r_mcbond_it 2.748 r_angle_refined_deg 1.484 r_nbtor_refined 0.305 r_nbd_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_refined 0.122 r_symmetry_nbd_refined 0.122 r_chiral_restr 0.112 r_ncsr_local_group_1 0.095 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3298 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms
Software Software Software Name Purpose DIALS data collection xia2 data reduction Aimless data scaling PHENIX phasing PHASER phasing Coot model building REFMAC refinement