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artificial mononuclear Zn-bound metalloprotein 3 (M3:Zn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZFG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.3 M MgCl2, MOPS pH 8.0, and 28 % w/v PEG 2000
Crystal Properties Matthews coefficient Solvent content 3.6 65.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.572 α = 90 b = 136.572 β = 90 c = 49.683 γ = 120
Symmetry Space Group P 3 2 1
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 2024-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979340 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 3.47 30 99.8 0.34 0.31 0.937 2.93 6.5 6986
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 3.47 3.68 1.563 0.836 0.836
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 3.47 29.57 6635 350 98.6 0.21673 0.21417 0.2213 0.26588 0.2786 RANDOM 82.201
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] -3.64 -1.82 -3.64 11.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.376 r_long_range_B_refined 13.553 r_long_range_B_other 13.553 r_mcangle_it 8.261 r_mcangle_other 8.26 r_scangle_other 8.254 r_dihedral_angle_1_deg 5.534 r_mcbond_it 5.084 r_mcbond_other 5.084 r_scbond_it 4.969
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.376 r_long_range_B_refined 13.553 r_long_range_B_other 13.553 r_mcangle_it 8.261 r_mcangle_other 8.26 r_scangle_other 8.254 r_dihedral_angle_1_deg 5.534 r_mcbond_it 5.084 r_mcbond_other 5.084 r_scbond_it 4.969 r_scbond_other 4.967 r_dihedral_angle_2_deg 3.339 r_angle_refined_deg 0.918 r_angle_other_deg 0.337 r_chiral_restr 0.039 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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 2605 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing