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Crystal structure of the Zn-induced tetramer of the engineered cyt cb562 variant RIDC-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM BIS-TRIS, 25% PEG 3350, 3.4 mM zinc chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.448 α = 90 b = 65.316 β = 104.7 c = 70.773 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 315r 2008-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.976 SSRL BL7-1
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 30.7 92.5 0.044 0.044 11.022 2.6 28830
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 2.11 92.4 0.176 0.176 2.7 2.5
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 (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 2QLA 2 30.7 28830 24925 1930 92.56 0.22788 0.22445 0.2255 0.27159 0.2305 RANDOM 26.016
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] 0.03 0.03 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.374 r_dihedral_angle_3_deg 18.618 r_dihedral_angle_4_deg 6.816 r_dihedral_angle_1_deg 4.514 r_scangle_it 1.718 r_angle_refined_deg 1.185 r_scbond_it 1.142 r_mcangle_it 0.692 r_mcbond_it 0.371 r_nbtor_refined 0.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.374 r_dihedral_angle_3_deg 18.618 r_dihedral_angle_4_deg 6.816 r_dihedral_angle_1_deg 4.514 r_scangle_it 1.718 r_angle_refined_deg 1.185 r_scbond_it 1.142 r_mcangle_it 0.692 r_mcbond_it 0.371 r_nbtor_refined 0.279 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.167 r_metal_ion_refined 0.091 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3268 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 180
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOLREP phasing