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Crystal Structure of a 16-Helix Bundle Architecture Produced by the Zinc-Mediated Self Assembly of Four Cytochrome cb562 Molecules
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BC5 PDB ENTRY 2BC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 100mM Tris, 1.25 mM ZnCl2, 25% PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.984 α = 90 b = 66.659 β = 90 c = 68.901 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 CCD APEX II CCD Miracol Monocapillary Beam Collimator 2007-03-16 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) R Merge 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 2.9 50 85.1 0.161 5.77 2.97 10032 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 2.99 66.2 0.42 1.5
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 THROUGHOUT PDB ENTRY 2BC5 2.9 50 550 8618 613 90.4 0.248 0.248 0.2447 0.295 0.298 random 44.124
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] -1.345 2.119 -0.774
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.883 c_mcangle_it 2.997 c_scbond_it 2.58 c_mcbond_it 1.747 c_angle_deg 1.331 c_bond_d 0.018 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.883 c_mcangle_it 2.997 c_scbond_it 2.58 c_mcbond_it 1.747 c_angle_deg 1.331 c_bond_d 0.018 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3276 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 176
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction APEX data collection SAINT data reduction CNS phasing