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Structure of reduced cytochrome c6 from Synechococcus sp. PCC 7002
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CTJ PDB ID 1CTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 292 10mM HEPES, 2.2M Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.98 37.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.879 α = 90 b = 82.879 β = 90 c = 28.277 γ = 120
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 MAR CCD 165 mm mirrors 2006-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8170 EMBL/DESY, HAMBURG X11
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 1.22 71.8 97.2 0.075 25.3 5 62938 62908 -3
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 1.22 1.26 73.4 0.373 2.4 2.7
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 (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 ID 1CTJ 1.23 19.58 62938 61634 1274 98.75 0.10771 0.10709 0.1553 0.13771 0.1818 RANDOM 7.467
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] -0.19 -0.1 -0.19 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.289 r_dihedral_angle_4_deg 19.982 r_sphericity_free 12.667 r_dihedral_angle_3_deg 11.107 r_dihedral_angle_1_deg 6.331 r_sphericity_bonded 4.407 r_scangle_it 4.306 r_scbond_it 3.315 r_mcangle_it 2.269 r_angle_refined_deg 1.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.289 r_dihedral_angle_4_deg 19.982 r_sphericity_free 12.667 r_dihedral_angle_3_deg 11.107 r_dihedral_angle_1_deg 6.331 r_sphericity_bonded 4.407 r_scangle_it 4.306 r_scbond_it 3.315 r_mcangle_it 2.269 r_angle_refined_deg 1.687 r_angle_other_deg 1.633 r_mcbond_it 1.619 r_rigid_bond_restr 1.418 r_mcbond_other 0.578 r_chiral_restr 0.106 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1986 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing