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Structure and metal-loading of a soluble periplasm cupro-protein: Cu- CucA-open
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 8 0.1M TRIS PH 8.0, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.57 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.413 α = 90 b = 55.836 β = 110.07 c = 63.034 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
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 1.8 46 99.9 0.06 14 3.8 26653 22
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 1.8 1.9 99.9 0.19 4.1 3.8
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 1.8 59.23 25190 1344 99.8 0.19607 0.19426 0.2319 0.22943 0.2625 RANDOM 35.168
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] -2.85 -1.22 0.83 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_4_deg 19.246 r_dihedral_angle_3_deg 12.156 r_dihedral_angle_1_deg 6.623 r_scangle_it 2.499 r_scbond_it 1.631 r_angle_refined_deg 1.276 r_mcangle_it 0.873 r_angle_other_deg 0.844 r_mcbond_it 0.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_4_deg 19.246 r_dihedral_angle_3_deg 12.156 r_dihedral_angle_1_deg 6.623 r_scangle_it 2.499 r_scbond_it 1.631 r_angle_refined_deg 1.276 r_mcangle_it 0.873 r_angle_other_deg 0.844 r_mcbond_it 0.527 r_mcbond_other 0.145 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_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 1782 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing