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Dimeric horse cytochrome c formed by refolding from molten globule state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 100mM Tris-HCl buffer, 200mM (NH4)2HPO4, 40%(v/v) PEG 200, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.948 α = 90 b = 94.145 β = 90 c = 36.39 γ = 90
Symmetry Space Group C 2 2 21
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 2013-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 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 1.8 50 97.4 10057 9791 -3
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 3WC8 1.8 30.48 9283 472 97.01 0.18311 0.18098 0.1794 0.22724 0.2268 RANDOM 27.239
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] -1.15 -1.97 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.061 r_dihedral_angle_4_deg 27.239 r_dihedral_angle_3_deg 15.992 r_dihedral_angle_1_deg 6.146 r_scangle_it 5.539 r_scbond_it 3.404 r_angle_refined_deg 1.997 r_mcangle_it 1.882 r_mcbond_it 1.048 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.061 r_dihedral_angle_4_deg 27.239 r_dihedral_angle_3_deg 15.992 r_dihedral_angle_1_deg 6.146 r_scangle_it 5.539 r_scbond_it 3.404 r_angle_refined_deg 1.997 r_mcangle_it 1.882 r_mcbond_it 1.048 r_chiral_restr 0.119 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 823 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 75
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing