☰ Navigation Tabs
Hydrogenobacter thermophilus cytochrome c552 dimer formed by domain swapping at C-terminal region
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 100 mM Tris-HCl, 200 mM sodium acetate, 30% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71 α = 90 b = 71.02 β = 90 c = 62.08 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 RAYONIX MX225HE 2015-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 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 1.3 30 100 0.113 6.8 3.9 38911
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 100 0.369 2.9 3.9
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 1YNR 1.3 30 37017 1877 99.91 0.17262 0.17113 0.181 0.2023 0.2096 RANDOM 10.554
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 0.79 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.939 r_sphericity_free 22.496 r_dihedral_angle_3_deg 11.553 r_dihedral_angle_4_deg 7.167 r_dihedral_angle_1_deg 5.096 r_sphericity_bonded 4.916 r_long_range_B_refined 2.12 r_long_range_B_other 1.74 r_angle_refined_deg 1.228 r_scangle_other 1.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.939 r_sphericity_free 22.496 r_dihedral_angle_3_deg 11.553 r_dihedral_angle_4_deg 7.167 r_dihedral_angle_1_deg 5.096 r_sphericity_bonded 4.916 r_long_range_B_refined 2.12 r_long_range_B_other 1.74 r_angle_refined_deg 1.228 r_scangle_other 1.072 r_mcangle_other 1.037 r_mcangle_it 1.031 r_scbond_other 0.959 r_scbond_it 0.958 r_rigid_bond_restr 0.939 r_mcbond_it 0.801 r_mcbond_other 0.795 r_angle_other_deg 0.72 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1205 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing