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artificial dinuclear Cu-bound metalloprotein 3 (D3: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 2.9 57.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.9 α = 110.83 b = 52.498 β = 107.43 c = 60.802 γ = 95.81
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 2024-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.003110 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.3 30 96.6 0.11 0.131 0.071 0.983 9.6 3.2 20609
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 95.3 0.34 0.414 0.233 0.893 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 29.93 2 20573 940 96.18 0.2011 0.1991 0.1991 0.2429 0.2428
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.988 f_angle_d 0.866 f_chiral_restr 0.057 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3024 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing