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The structure of Cu(II)-CopC from Thioalkalivibrio paradoxus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N1T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 288 0.2M Ammonium formate pH 6.6, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.02 38.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.241 α = 90 b = 38.275 β = 90.33 c = 104.666 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2019-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.999 SPring-8 BL41XU
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 1.8 104.66 100 0.129 0.14 0.054 0.995 6.4 6.5 21085
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 1.8 1.84 99.3 0.735 0.798 0.307 0.858 6.6
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 1.8 52.39 19980 1015 99.71 0.18775 0.18564 0.1947 0.22996 0.2372 RANDOM 30.966
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] 3.23 -1.52 -1.41 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.128 r_dihedral_angle_2_deg 8.455 r_long_range_B_other 7.275 r_long_range_B_refined 7.269 r_dihedral_angle_1_deg 6.938 r_scangle_other 5.563 r_scbond_it 3.679 r_scbond_other 3.677 r_mcangle_it 3.332 r_mcangle_other 3.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.128 r_dihedral_angle_2_deg 8.455 r_long_range_B_other 7.275 r_long_range_B_refined 7.269 r_dihedral_angle_1_deg 6.938 r_scangle_other 5.563 r_scbond_it 3.679 r_scbond_other 3.677 r_mcangle_it 3.332 r_mcangle_other 3.332 r_mcbond_it 2.447 r_mcbond_other 2.443 r_angle_refined_deg 1.971 r_angle_other_deg 0.703 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1933 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing