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Trimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 2.0 M ammonium sulfate with 2% (v/v) PEG 400, 100 mM HEPES buffer
Crystal Properties Matthews coefficient Solvent content 3.67 66.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.804 α = 90 b = 153.804 β = 90 c = 153.804 γ = 90
Symmetry Space Group F 4 3 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 RAYONIX MX-225 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) 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 1.7 50 96 23.839 18.6 19058
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 1.7 1.73 100
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 2zxy 1.7 50 15942 881 94.81 0.22905 0.22693 0.2354 0.26831 0.2696 RANDOM 20.177
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.836 r_sphericity_free 28.913 r_dihedral_angle_4_deg 18.379 r_dihedral_angle_3_deg 13.159 r_sphericity_bonded 7.732 r_dihedral_angle_1_deg 4.706 r_long_range_B_refined 2.882 r_long_range_B_other 2.513 r_angle_refined_deg 2.158 r_scangle_other 2.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.836 r_sphericity_free 28.913 r_dihedral_angle_4_deg 18.379 r_dihedral_angle_3_deg 13.159 r_sphericity_bonded 7.732 r_dihedral_angle_1_deg 4.706 r_long_range_B_refined 2.882 r_long_range_B_other 2.513 r_angle_refined_deg 2.158 r_scangle_other 2.006 r_rigid_bond_restr 1.846 r_mcangle_it 1.675 r_mcangle_other 1.674 r_scbond_it 1.651 r_scbond_other 1.65 r_mcbond_it 1.231 r_mcbond_other 1.23 r_angle_other_deg 0.899 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 723 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing