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Tetrameric Allochromatium vinosum cytochrome c'
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 0.1mM sodium acetate, 0.2mM ammonium acetate, 30% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.949 α = 90 b = 48.62 β = 92.28 c = 130.55 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 CCD RAYONIX MX225HE 2016-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 1.6 41.4 98.6 0.069 7.9 3.7 135869
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 1.6 1.69 97.2 0.325 2.9 3.6
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 1bbh 1.6 41.4 129158 6704 98.58 0.20546 0.20406 0.2129 0.23228 0.2383 RANDOM 26.97
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] -1.38 0.18 2.02 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.263 r_sphericity_free 33.251 r_dihedral_angle_3_deg 16.277 r_sphericity_bonded 14.602 r_dihedral_angle_4_deg 10.787 r_long_range_B_refined 5.153 r_rigid_bond_restr 5.015 r_long_range_B_other 4.901 r_scangle_other 4.427 r_mcangle_it 4.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.263 r_sphericity_free 33.251 r_dihedral_angle_3_deg 16.277 r_sphericity_bonded 14.602 r_dihedral_angle_4_deg 10.787 r_long_range_B_refined 5.153 r_rigid_bond_restr 5.015 r_long_range_B_other 4.901 r_scangle_other 4.427 r_mcangle_it 4.349 r_mcangle_other 4.349 r_dihedral_angle_1_deg 4.118 r_scbond_it 3.673 r_scbond_other 3.673 r_mcbond_it 3.554 r_mcbond_other 3.551 r_angle_other_deg 1.387 r_angle_refined_deg 1.331 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 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 7736 Nucleic Acid Atoms Solvent Atoms 808 Heterogen Atoms 344
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing