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artificial mononuclear Cu-bound metalloprotein 6 (M6:Cu)
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 2.52 51.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.467 α = 100.87 b = 52.25 β = 100.39 c = 55.88 γ = 112.11
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 2024-05-16 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 2.49 27.36 97 0.032 0.045 0.997 10.72 3.49 14194
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 2.49 2.64 0.058 0.082 0.991
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 2.49 27.36 13484 710 96.97 0.23469 0.23171 0.2391 0.29039 0.3006 RANDOM 26.084
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] 4.41 -0.06 -1.63 -1.89 -1.15 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.085 r_long_range_B_refined 7.044 r_long_range_B_other 7.03 r_dihedral_angle_1_deg 6.785 r_dihedral_angle_2_deg 6.637 r_scangle_other 4.328 r_mcangle_it 3.262 r_mcangle_other 3.262 r_scbond_it 2.567 r_scbond_other 2.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.085 r_long_range_B_refined 7.044 r_long_range_B_other 7.03 r_dihedral_angle_1_deg 6.785 r_dihedral_angle_2_deg 6.637 r_scangle_other 4.328 r_mcangle_it 3.262 r_mcangle_other 3.262 r_scbond_it 2.567 r_scbond_other 2.566 r_mcbond_it 1.988 r_mcbond_other 1.988 r_angle_refined_deg 1.341 r_angle_other_deg 0.49 r_chiral_restr 0.066 r_bond_refined_d 0.006 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 3036 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing