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Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, A104/57G AB3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 27% (+/-)-2-methyl-2,4-pentanediol 400 in 100 mM Bis-Tris (pH 6.5) with 0.2M CaCl2 and 20 mM ampicillin
Crystal Properties Matthews coefficient Solvent content 3.46 64.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.313 α = 90 b = 92.213 β = 90 c = 98.599 γ = 90
Symmetry Space Group F 2 2 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 MARMOSAIC 325 mm CCD 2014-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.98 SSRL BL14-1
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 2.8 35.66 98.9 0.048 0.048 22.2 4.3 4159
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 2.8 8.86 98.9 0.048 0.168 22.2 4.3
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 2BC5 2.8 35.66 4104 184 98.6 0.239 0.237 0.24 0.285 0.2848 RANDOM 57
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] 0.89 -0.34 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_3_deg 14.974 r_dihedral_angle_4_deg 7.817 r_dihedral_angle_1_deg 3.489 r_mcangle_it 2.221 r_mcbond_other 1.221 r_mcbond_it 1.22 r_angle_refined_deg 0.906 r_angle_other_deg 0.714 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_3_deg 14.974 r_dihedral_angle_4_deg 7.817 r_dihedral_angle_1_deg 3.489 r_mcangle_it 2.221 r_mcbond_other 1.221 r_mcbond_it 1.22 r_angle_refined_deg 0.906 r_angle_other_deg 0.714 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_bond_other_d 0.006 r_gen_planes_refined 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 712 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling