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Structure and metal-loading of a soluble periplasm cupro-protein: Cu- CucA-closed (SeMet)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XL9 PDB ENTRY 2XL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M HEPES PH 7.5, 20% (W/V) PEG 8000, 0.5MM CUSO4
Crystal Properties Matthews coefficient Solvent content 3.87 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.483 α = 90 b = 88.483 β = 90 c = 192.419 γ = 120
Symmetry Space Group P 64 2 2
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 QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.4 60 99.7 0.1 13.6 6 18072 32
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 2.4 2.53 100 0.34 4.9 6.1
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 2XL9 2.4 44.24 17157 913 99.3 0.17609 0.17417 0.1904 0.21317 0.2271 RANDOM 31.312
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] 0.28 0.14 0.28 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.558 r_dihedral_angle_4_deg 22.08 r_dihedral_angle_3_deg 12.567 r_dihedral_angle_1_deg 6.229 r_scangle_it 3.099 r_scbond_it 1.872 r_angle_refined_deg 1.298 r_mcangle_it 1.117 r_mcbond_it 0.566 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.558 r_dihedral_angle_4_deg 22.08 r_dihedral_angle_3_deg 12.567 r_dihedral_angle_1_deg 6.229 r_scangle_it 3.099 r_scbond_it 1.872 r_angle_refined_deg 1.298 r_mcangle_it 1.117 r_mcbond_it 0.566 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1848 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing