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artificial mononuclear Zn-bound metalloprotein 1 (M1:Mn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.3 M MgCl2, 0.1 M MOPS pH 8.0, and 28 % w/v PEG 2000
Crystal Properties Matthews coefficient Solvent content 3.66 66.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.81 α = 90 b = 136.81 β = 90 c = 50.067 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2024-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979330 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.29 30 99.8 0.046 0.065 0.996 6.4 10.2 46903
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.43 0.362 0.512 0.798
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.29 29.62 44553 2345 99.76 0.18353 0.18156 0.1914 0.22099 0.2271 RANDOM 41.587
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] -1.26 -0.63 -1.26 4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.299 r_long_range_B_other 9.448 r_long_range_B_refined 9.44 r_scangle_other 7.484 r_dihedral_angle_1_deg 6.966 r_dihedral_angle_2_deg 5.562 r_mcangle_other 5.423 r_mcangle_it 5.422 r_scbond_it 4.892 r_scbond_other 4.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.299 r_long_range_B_other 9.448 r_long_range_B_refined 9.44 r_scangle_other 7.484 r_dihedral_angle_1_deg 6.966 r_dihedral_angle_2_deg 5.562 r_mcangle_other 5.423 r_mcangle_it 5.422 r_scbond_it 4.892 r_scbond_other 4.892 r_mcbond_it 3.947 r_mcbond_other 3.945 r_angle_refined_deg 1.538 r_angle_other_deg 0.555 r_chiral_restr 0.079 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5218 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing