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A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Monoclinic Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QLA PDB entry 2QLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 25% PEG2000, 0.2 M NaCl, 0.1 M TRIS, 3.3 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.68 54.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.339 α = 90 b = 107.396 β = 105.52 c = 102.051 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 QUANTUM 315 Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) 2008-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97607 SSRL BL9-1
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 2.4 98.533 97.2 0.096 0.096 6.464 2.7 56311 55485 2 2
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 2.4 2.53 97 0.552 0.552 1.3 2.6 8079
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB entry 2QLA 2.4 98.53 57214 55103 3980 96.31 0.213 0.213 0.209 0.2097 0.268 0.2686 RANDOM 41.455
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] 0.1 0.11 -0.15 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.25 r_dihedral_angle_3_deg 19.263 r_dihedral_angle_4_deg 13.467 r_dihedral_angle_1_deg 5.06 r_scangle_it 1.714 r_angle_refined_deg 1.246 r_scbond_it 1.142 r_mcangle_it 0.63 r_mcbond_it 0.37 r_nbtor_other 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.25 r_dihedral_angle_3_deg 19.263 r_dihedral_angle_4_deg 13.467 r_dihedral_angle_1_deg 5.06 r_scangle_it 1.714 r_angle_refined_deg 1.246 r_scbond_it 1.142 r_mcangle_it 0.63 r_mcbond_it 0.37 r_nbtor_other 0.324 r_angle_other_deg 0.317 r_nbtor_refined 0.278 r_symmetry_vdw_refined 0.223 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.14 r_nbd_other 0.093 r_chiral_restr 0.075 r_mcbond_other 0.046 r_metal_ion_refined 0.018 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9648 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 756
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing