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Crystal structure of low-redox-potential cytochrom c6 from brown alga Hizikia fusiformis at 1.6 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GDV PDB ENTRY 1GDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 293 0.1M CAPS pH 10.5, 0.2M Li2SO4, 2.2M AmSO4, 3% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.79 67.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.578 α = 90 b = 84.578 β = 90 c = 232.911 γ = 90
Symmetry Space Group P 41 21 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 ADSC QUANTUM 315 2006-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 50 107513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66
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 PDB ENTRY 1GDV 1.6 20 101892 5347 100 0.18518 0.18394 0.1853 0.20906 0.2104 RANDOM 22.315
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] -0.14 -0.14 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.436 r_dihedral_angle_4_deg 13.005 r_dihedral_angle_3_deg 12.292 r_dihedral_angle_1_deg 4.649 r_scangle_it 3.31 r_scbond_it 2.208 r_mcangle_it 1.345 r_angle_refined_deg 1.165 r_mcbond_it 0.779 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.436 r_dihedral_angle_4_deg 13.005 r_dihedral_angle_3_deg 12.292 r_dihedral_angle_1_deg 4.649 r_scangle_it 3.31 r_scbond_it 2.208 r_mcangle_it 1.345 r_angle_refined_deg 1.165 r_mcbond_it 0.779 r_nbtor_refined 0.295 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.188 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3834 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 278
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing