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Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)(CO)2Cl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 293 15 mg/ml protei solution mixed with 1.8 M ammonium sulfate, 100 mM sodium acetate pH 4.7
Crystal Properties Matthews coefficient Solvent content 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.303 α = 90 b = 93.606 β = 90 c = 124.211 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 315r 2015-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979769 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 46.8 98.8 0.057 21.24 4.98 92563 27.6
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 1ZLQ 1.8 46.8 87934 4629 98.77 0.16972 0.16769 0.1793 0.20818 0.1948 RANDOM 27.073
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] 1.24 -1.05 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.328 r_dihedral_angle_4_deg 16.472 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_1_deg 6.608 r_long_range_B_other 6.229 r_long_range_B_refined 6.228 r_scangle_other 4.812 r_scbond_it 3.317 r_scbond_other 3.317 r_mcangle_it 3.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.328 r_dihedral_angle_4_deg 16.472 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_1_deg 6.608 r_long_range_B_other 6.229 r_long_range_B_refined 6.228 r_scangle_other 4.812 r_scbond_it 3.317 r_scbond_other 3.317 r_mcangle_it 3.224 r_mcangle_other 3.224 r_mcbond_it 2.434 r_mcbond_other 2.412 r_angle_other_deg 2.347 r_angle_refined_deg 1.898 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_other 0.013 r_gen_planes_refined 0.011 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7847 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing