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Crystal Structure of Cytochrome c555 from Aquifex aeolicus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 39% PEG 4000, 0.8M ammonium acetate, 0.1M tri-sodium citrate dehydrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.94 36.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.529 α = 90 b = 32.993 β = 115.05 c = 49.668 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU JUPITER 210 2007-11-27 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RIGAKU JUPITER 210 2007-11-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.7 SPring-8 BL38B1 2 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.73786, 1.74011, 1.69260 SPring-8 BL38B1
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 1.15 50 97 0.047 3.71 25402
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.15 1.19 89.4 10.01
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.15 15.92 23375 1257 97.56 0.12899 0.12711 0.1261 0.16386 0.1615 RANDOM 10.536
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.677 r_sphericity_free 14.002 r_dihedral_angle_3_deg 13.816 r_dihedral_angle_1_deg 12.278 r_sphericity_bonded 6.455 r_scangle_it 6.241 r_scbond_it 4.903 r_mcangle_it 3.579 r_rigid_bond_restr 3.165 r_mcbond_it 2.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.677 r_sphericity_free 14.002 r_dihedral_angle_3_deg 13.816 r_dihedral_angle_1_deg 12.278 r_sphericity_bonded 6.455 r_scangle_it 6.241 r_scbond_it 4.903 r_mcangle_it 3.579 r_rigid_bond_restr 3.165 r_mcbond_it 2.628 r_angle_refined_deg 0.93 r_nbd_refined 0.342 r_symmetry_vdw_refined 0.328 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.26 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.057 r_gen_planes_refined 0.023 r_bond_refined_d 0.01 r_metal_ion_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 711 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling SHELXS phasing