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Identification of zinc ions in LMO4.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RUT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.25 M Sodium Malonate pH 7, 20 % v/w PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.816 α = 90 b = 61.816 β = 90 c = 93.396 γ = 120
Symmetry Space Group P 3 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2023-05-25 M SINGLE WAVELENGTH 2 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2023-05-25 M SINGLE WAVELENGTH 3 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2023-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 1.2853 Diamond I23 2 SYNCHROTRON DIAMOND BEAMLINE I23 1.2874 Diamond I23 3 SYNCHROTRON DIAMOND BEAMLINE I23 1.3051 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 53.534 100 0.11 1 18.4 18.8 19257
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 3.08 0.35 0.5
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 1.8 53.534 19198 967 99.72 0.2 0.1983 0.205 0.2335 0.2404 46.685
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] -0.124 -0.062 -0.124 0.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.259 r_dihedral_angle_3_deg 13.119 r_lrange_it 10.091 r_scangle_it 8.48 r_dihedral_angle_1_deg 6.21 r_scbond_it 5.982 r_mcangle_it 5.707 r_mcbond_it 4.305 r_dihedral_angle_2_deg 3.868 r_angle_refined_deg 1.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.259 r_dihedral_angle_3_deg 13.119 r_lrange_it 10.091 r_scangle_it 8.48 r_dihedral_angle_1_deg 6.21 r_scbond_it 5.982 r_mcangle_it 5.707 r_mcbond_it 4.305 r_dihedral_angle_2_deg 3.868 r_angle_refined_deg 1.659 r_nbtor_refined 0.308 r_xyhbond_nbd_refined 0.2 r_nbd_refined 0.198 r_symmetry_nbd_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.131 r_chiral_restr 0.096 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1273 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing