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Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 290 0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.34 47.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.514 α = 90 b = 146.514 β = 90 c = 114.59 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD MARMOSAIC 225 mm CCD 2011-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 50 100 0.14 0.157 14.6 5.8 160488 3 3 35.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 0.71 0.691 3.2 5.7 8050
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XC1 2.1 47.96 3 160488 152214 8174 99.78 0.168 0.14423 0.14285 0.1464 0.16941 0.1676 RANDOM 28.275
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] 9.41 9.41 -18.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.087 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 18.453 r_dihedral_angle_1_deg 6.28 r_scangle_it 5.145 r_scbond_it 3.919 r_mcangle_it 2.528 r_mcbond_it 1.786 r_angle_refined_deg 1.726 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.087 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 18.453 r_dihedral_angle_1_deg 6.28 r_scangle_it 5.145 r_scbond_it 3.919 r_mcangle_it 2.528 r_mcbond_it 1.786 r_angle_refined_deg 1.726 r_chiral_restr 0.121 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21402 Nucleic Acid Atoms Solvent Atoms 1469 Heterogen Atoms 18
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling