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Crystal structure of NikA from Staphylococcus aureus in complex with Ni-(L-His)(2-methyl-thiazolidine dicarboxylate) (co-crystallization with Ni(II) and CDdeltaHis medium supernatant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 27% PEG 3350, 0.1 M HEPES pH 7.0 - protein pre-incubated with NiCl2 and CDdeltaHis medium supernatant.
Crystal Properties Matthews coefficient Solvent content 2.25 45.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.803 α = 90 b = 67.373 β = 90 c = 115.566 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 100 PIXEL DECTRIS PILATUS 6M-F 2013-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
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 1.75 45.54 96.6 0.078 14.6 4.4 47766 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 96.4 0.616 3.36 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 4OFJ 1.75 45.543 1.37 47756 2388 96.62 0.1732 0.1716 0.1747 0.2028 0.2041 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.377 f_angle_d 1.125 f_chiral_restr 0.053 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3704 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 148
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing Coot model building XSCALE data scaling