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Visualising the Metal-binding Versatility of Copper Trafficking Sites: Atx1 side-to-side (anaerobic)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XMJ PDB ENTRY 2XMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 24 % (W/V) PEG 8000, 200 MM SODIUM ACETATE, 100 MM SODIUM CACODYLATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.991 α = 90 b = 41.709 β = 107.49 c = 55.791 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 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.35 53.22 97.4 0.08 15.4 4.9 29653 10
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.42 95.9 0.29 5.1 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2XMJ 1.35 53.22 28177 1443 97.21 0.13055 0.1294 0.1384 0.15274 0.1679 RANDOM 8.829
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] 0.35 -0.34 -0.16 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.164 r_dihedral_angle_3_deg 10.923 r_sphericity_free 7.026 r_dihedral_angle_1_deg 5.567 r_scangle_it 5.476 r_dihedral_angle_4_deg 4.929 r_scbond_it 3.538 r_sphericity_bonded 3.441 r_mcangle_it 2.721 r_mcbond_it 1.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.164 r_dihedral_angle_3_deg 10.923 r_sphericity_free 7.026 r_dihedral_angle_1_deg 5.567 r_scangle_it 5.476 r_dihedral_angle_4_deg 4.929 r_scbond_it 3.538 r_sphericity_bonded 3.441 r_mcangle_it 2.721 r_mcbond_it 1.694 r_rigid_bond_restr 1.446 r_angle_refined_deg 1.442 r_angle_other_deg 1.006 r_mcbond_other 0.62 r_symmetry_vdw_refined 0.373 r_nbd_refined 0.232 r_symmetry_vdw_other 0.18 r_nbd_other 0.178 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.113 r_metal_ion_refined 0.098 r_chiral_restr 0.097 r_nbtor_other 0.088 r_symmetry_metal_ion_refined 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 887 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing