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Crystal Structure of a Ni-directed Dimer of Cytochrome cb562 with a Quinolate-Histidine Hybrid Coordination Motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BC5 monomer of 2BC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100 mM Tris, 25% PEG 1500, 1.05 mM nickel(II) sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.04 59.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.44 α = 90 b = 34.511 β = 90 c = 46.896 γ = 90
Symmetry Space Group P 21 21 2
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 APEX II CCD 2009-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE SIEMENS 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99 6832 6761 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.36 95.3
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 througout monomer of 2BC5 2.3 50 2 6803 6441 503 94.7 0.27 0.27 0.266 0.2588 0.314 0.3044 random 30.439
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 c_scangle_it 3.469 c_mcangle_it 2.465 c_scbond_it 2.402 c_mcbond_it 1.555 c_angle_deg 1.21 c_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 822 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 59
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction APEX data collection SAINT data reduction SADABS data scaling MOLREP phasing