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Crystal structure of cytochrome c6 Q57V mutant from Synechococcus sp. PCC 7002
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DR0 PDB ENTRY 3DR0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 2.2M Ammonium sulphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.02 39.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.781 α = 90 b = 27.637 β = 101.16 c = 44.099 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MAR555 FLAT PANEL mirrors 2010-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8166 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 1.13 50 99.1 0.05 15.3 3.3 28144 28144 -3 13.3
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 1.13 1.2 96.8 0.451 2 1.7 4430
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 (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 3DR0 1.13 43.26 27159 27159 986 100 0.13931 0.13931 0.13797 0.1446 0.17574 0.1757 RANDOM 7.156
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] 0.18 0.85 0.08 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.816 r_dihedral_angle_4_deg 20.177 r_dihedral_angle_3_deg 10.14 r_dihedral_angle_1_deg 5.598 r_scangle_it 4.272 r_scbond_it 3.356 r_mcangle_it 2.364 r_angle_refined_deg 1.872 r_mcbond_it 1.8 r_rigid_bond_restr 1.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.816 r_dihedral_angle_4_deg 20.177 r_dihedral_angle_3_deg 10.14 r_dihedral_angle_1_deg 5.598 r_scangle_it 4.272 r_scbond_it 3.356 r_mcangle_it 2.364 r_angle_refined_deg 1.872 r_mcbond_it 1.8 r_rigid_bond_restr 1.528 r_angle_other_deg 1.244 r_mcbond_other 0.872 r_chiral_restr 0.127 r_bond_refined_d 0.023 r_gen_planes_refined 0.016 r_gen_planes_other 0.009 r_bond_other_d 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 660 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 55
Software Software Software Name Purpose AUTOMAR data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling