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Crystal structure of cytochrome c6B from Synechococcus sp. WH8102
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EIF PDB ENTRY 4EIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 2.2 M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.07 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.11 α = 90 b = 28.98 β = 92.3 c = 24.68 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 RAYONIX MX225HE mirrors 2012-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.4 27.95 97.9 0.059 13.8 3.6 14665 14663 -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 1.4 1.49 90.1 0.559 2.02 3.1
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 R-FREE PDB ENTRY 4EIF 1.4 27.95 13712 13712 950 97.9 0.12398 0.12003 0.1216 0.18102 0.1871 RANDOM 15.413
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] 0.56 -0.02 0.29 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.2 r_sphericity_free 22.466 r_dihedral_angle_4_deg 22.019 r_dihedral_angle_3_deg 12.451 r_sphericity_bonded 8.977 r_dihedral_angle_1_deg 5.02 r_rigid_bond_restr 4.309 r_scbond_it 3.152 r_mcangle_it 2.313 r_mcbond_it 1.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.2 r_sphericity_free 22.466 r_dihedral_angle_4_deg 22.019 r_dihedral_angle_3_deg 12.451 r_sphericity_bonded 8.977 r_dihedral_angle_1_deg 5.02 r_rigid_bond_restr 4.309 r_scbond_it 3.152 r_mcangle_it 2.313 r_mcbond_it 1.946 r_mcbond_other 1.942 r_angle_refined_deg 1.769 r_angle_other_deg 0.965 r_chiral_restr 0.116 r_gen_planes_other 0.026 r_gen_planes_refined 0.019 r_bond_refined_d 0.016 r_bond_other_d 0.004 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 643 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 44
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling