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artificial mononuclear Zn-bound metalloprotein 4 (M4:Zn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Li2SO4, 20 % PEG 4000, pH 8.0 0.1M MOPS
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.43 α = 90 b = 52.44 β = 114.56 c = 81.84 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M 2024-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.979420 PAL/PLS 11C
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 2.59 30 97.6 0.084 0.118 0.981 5.03 3.4 12265
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 2.59 2.75 0.263 0.371 0.615
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 2.66 29.3 12265 646 97.57 0.21318 0.21075 0.2126 0.25981 0.259 RANDOM 48.221
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] -2.66 1.04 -2.24 2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.796 r_long_range_B_refined 10.543 r_long_range_B_other 10.542 r_scangle_other 7.19 r_dihedral_angle_1_deg 6.829 r_mcangle_it 5.402 r_mcangle_other 5.401 r_scbond_it 4.484 r_scbond_other 4.483 r_dihedral_angle_2_deg 4.467
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.796 r_long_range_B_refined 10.543 r_long_range_B_other 10.542 r_scangle_other 7.19 r_dihedral_angle_1_deg 6.829 r_mcangle_it 5.402 r_mcangle_other 5.401 r_scbond_it 4.484 r_scbond_other 4.483 r_dihedral_angle_2_deg 4.467 r_mcbond_it 3.61 r_mcbond_other 3.61 r_angle_refined_deg 1.379 r_angle_other_deg 0.517 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.004 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 3036 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing