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Crystal structure of the Cu-induced dimer of the engineered cyt cb562 variant RIDC-1
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 7.5 293 100 mM HEPES, 200 mM sodium chloride, 25% PEG 3350, 10.7 mM copper sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.165 α = 90 b = 87.045 β = 90 c = 80.765 γ = 90
Symmetry Space Group C 2 2 21
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 2008-08-28 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) 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 2.2 22.2 98.7 0.168 0.168 6.5 3.12 12174 12016
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 2.3 96.5 0.48 0.48 2 1.7 1473
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 MOLECULAR REPLACEMENT THROUGHOUT 2QLA 2.2 22.2 12174 11999 832 98.84 0.208 0.208 0.204 0.2091 0.27 0.2646 RANDOM 13.357
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] -0.04 0.08 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.337 r_dihedral_angle_3_deg 19.146 r_dihedral_angle_4_deg 10.924 r_dihedral_angle_1_deg 4.644 r_scangle_it 1.87 r_scbond_it 1.178 r_angle_refined_deg 1.104 r_mcangle_it 0.676 r_mcbond_it 0.373 r_nbtor_refined 0.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.337 r_dihedral_angle_3_deg 19.146 r_dihedral_angle_4_deg 10.924 r_dihedral_angle_1_deg 4.644 r_scangle_it 1.87 r_scbond_it 1.178 r_angle_refined_deg 1.104 r_mcangle_it 0.676 r_mcbond_it 0.373 r_nbtor_refined 0.282 r_symmetry_hbond_refined 0.217 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.075 r_metal_ion_refined 0.02 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1638 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction APEX data collection SAINT data reduction SADABS data scaling MOLREP phasing