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Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 351C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M HEPES-NaOH buffer containing 1.4M sodium citrate tribasic dehydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.611 α = 90 b = 82.611 β = 90 c = 89.828 γ = 120
Symmetry Space Group P 63 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 ADSC QUANTUM 315 2010-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.8 SPring-8 BL38B1
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 1.5 50 99.9 0.062 0.062 57.942 20.7 30970 29583 -3
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 1.5 1.55 100 0.551 0.551 7.026 20.6 2893
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 351C 1.5 50 27950 1495 99.51 0.14178 0.13946 0.1403 0.18814 0.1877 RANDOM 28.196
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] 0.52 0.26 0.52 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.52 r_sphericity_free 30.695 r_sphericity_bonded 15.869 r_dihedral_angle_3_deg 11.435 r_dihedral_angle_4_deg 9.369 r_dihedral_angle_1_deg 5.604 r_long_range_B_refined 5.138 r_scangle_other 4.719 r_long_range_B_other 4.618 r_scbond_it 4.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.52 r_sphericity_free 30.695 r_sphericity_bonded 15.869 r_dihedral_angle_3_deg 11.435 r_dihedral_angle_4_deg 9.369 r_dihedral_angle_1_deg 5.604 r_long_range_B_refined 5.138 r_scangle_other 4.719 r_long_range_B_other 4.618 r_scbond_it 4.161 r_scbond_other 4.15 r_mcangle_other 3.858 r_mcangle_it 3.844 r_mcbond_it 3.167 r_mcbond_other 3.092 r_rigid_bond_restr 2.696 r_angle_refined_deg 1.604 r_angle_other_deg 0.931 r_chiral_restr 0.137 r_gen_planes_other 0.014 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1220 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 86
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling