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cytochrome c3 from Desulfomicrobium baculatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CY3 PDB ENTRY 2CY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 25% PEG 6K, 0.1 M TRIS-HCL, PH 7.5-8.0
Crystal Properties Matthews coefficient Solvent content 2.66 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43 α = 90 b = 43 β = 90 c = 64.7 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE MARRESEARCH 1992-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.5 SRS PX9.5
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 1.81 21.5 94.4 0.08 9.1 1.9 11633
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 1.81 1.9 80 0.183 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 PDB ENTRY 2CY3 1.81 20.41 10752 876 94.7 0.178 0.176 0.1811 0.199 0.1892 RANDOM 24.73
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.33 r_scangle_it 4.218 r_scbond_it 2.789 r_mcangle_it 2.267 r_angle_refined_deg 1.948 r_mcbond_it 1.353 r_angle_other_deg 1.069 r_nbd_refined 0.398 r_symmetry_vdw_other 0.377 r_nbd_other 0.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.33 r_scangle_it 4.218 r_scbond_it 2.789 r_mcangle_it 2.267 r_angle_refined_deg 1.948 r_mcbond_it 1.353 r_angle_other_deg 1.069 r_nbd_refined 0.398 r_symmetry_vdw_other 0.377 r_nbd_other 0.251 r_chiral_restr 0.155 r_xyhbond_nbd_refined 0.104 r_symmetry_vdw_refined 0.098 r_nbtor_other 0.093 r_symmetry_hbond_refined 0.048 r_bond_other_d 0.037 r_bond_refined_d 0.022 r_metal_ion_refined 0.017 r_gen_planes_refined 0.016 r_gen_planes_other 0.005 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other 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 878 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing