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artificial mononuclear Zn-bound metalloprotein 2 (M2: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, 0.1 M MOPS pH 8.0, and 28 % w/v PEG 2000
Crystal Properties Matthews coefficient Solvent content 3.53 65.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.12 α = 90 b = 136.12 β = 90 c = 48.88 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 2023-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.000030 PAL/PLS 5C (4A)
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 2.86 30 99.8 0.09 0.127 0.985 4.24 5.4 23436
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 2.86 3.03 0.538 0.761 0.573
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.86 29.47 22259 1172 99.77 0.19662 0.19376 0.24989 0.2572 RANDOM 64.665
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] -0.82 -0.41 -0.82 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.903 r_long_range_B_refined 11.958 r_long_range_B_other 11.958 r_scangle_other 8.304 r_dihedral_angle_1_deg 6.93 r_mcangle_other 6.907 r_mcangle_it 6.905 r_scbond_it 5.24 r_scbond_other 5.239 r_dihedral_angle_2_deg 4.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.903 r_long_range_B_refined 11.958 r_long_range_B_other 11.958 r_scangle_other 8.304 r_dihedral_angle_1_deg 6.93 r_mcangle_other 6.907 r_mcangle_it 6.905 r_scbond_it 5.24 r_scbond_other 5.239 r_dihedral_angle_2_deg 4.862 r_mcbond_it 4.558 r_mcbond_other 4.553 r_angle_refined_deg 1.296 r_angle_other_deg 0.462 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 5040 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing