☰ Navigation Tabs
Crystal structure of the cytochrome c-552 from Hydrogenobacter thermophilus at 2.0 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 451C PDB ENTRY 451C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 MPD, ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.36 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.712 α = 90 b = 56.712 β = 90 c = 220.179 γ = 90
Symmetry Space Group P 43 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 MARRESEARCH 2003-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 56 98.1 0.069 25401 25401
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 2 2.07 88.4 0.292
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 451C 2 25 1 23720 23720 1270 98.38 0.1728 0.17287 0.17054 0.1753 0.21777 0.2194 RANDOM 12.369
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] -0.33 -0.33 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.242 r_dihedral_angle_4_deg 22.966 r_dihedral_angle_3_deg 15.693 r_dihedral_angle_1_deg 5.41 r_scangle_it 3.053 r_scbond_it 2.085 r_angle_refined_deg 1.566 r_mcangle_it 1.267 r_mcbond_it 0.784 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.242 r_dihedral_angle_4_deg 22.966 r_dihedral_angle_3_deg 15.693 r_dihedral_angle_1_deg 5.41 r_scangle_it 3.053 r_scbond_it 2.085 r_angle_refined_deg 1.566 r_mcangle_it 1.267 r_mcbond_it 0.784 r_nbtor_refined 0.31 r_nbd_refined 0.282 r_symmetry_vdw_refined 0.244 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2384 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 251
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing