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Structure and metal-loading of a soluble periplasm cupro-protein: apo- 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 0.1M HEPES PH7.7, 18% PEG 8000, 1MM EDTA, PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.431 α = 90 b = 142.473 β = 95.14 c = 63.498 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 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.3 47 98.7 0.09 8.4 2.5 44448 39
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 2.3 2.42 99.1 0.31 3.2 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XL9 2.3 40.66 42199 2220 98.61 0.18674 0.18453 0.22864 0.2736 RANDOM 51.631
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] 0.26 1.52 -0.35 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.16 r_dihedral_angle_4_deg 21.517 r_dihedral_angle_3_deg 14.344 r_dihedral_angle_1_deg 6.512 r_scangle_it 2.641 r_scbond_it 1.838 r_angle_refined_deg 1.29 r_mcangle_it 0.911 r_angle_other_deg 0.871 r_mcbond_it 0.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.16 r_dihedral_angle_4_deg 21.517 r_dihedral_angle_3_deg 14.344 r_dihedral_angle_1_deg 6.512 r_scangle_it 2.641 r_scbond_it 1.838 r_angle_refined_deg 1.29 r_mcangle_it 0.911 r_angle_other_deg 0.871 r_mcbond_it 0.471 r_mcbond_other 0.092 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 7262 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing