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Structure of Desulfovibrio desulfuricans G20 tetraheme cytochrome with bound molybdate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 20% PEG 4000, 5% ethylene glycol, 0.2M ZnCl2, 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.92 36.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.16 α = 90 b = 43.7 β = 90 c = 57.887 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.2 30 96.5 0.097 5706
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 2.2 2.28 94.1 0.523
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2A3M 2.3 27.13 4479 4479 482 98.51 0.19668 0.197 0.191 0.1933 0.248 0.2495 RANDOM 37.371
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] 0.89 1.33 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.083 r_dihedral_angle_3_deg 17.388 r_dihedral_angle_1_deg 5.792 r_scangle_it 4.006 r_dihedral_angle_4_deg 3.962 r_scbond_it 3.193 r_mcangle_it 2.572 r_angle_refined_deg 1.856 r_mcbond_it 1.628 r_nbtor_refined 0.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.083 r_dihedral_angle_3_deg 17.388 r_dihedral_angle_1_deg 5.792 r_scangle_it 4.006 r_dihedral_angle_4_deg 3.962 r_scbond_it 3.193 r_mcangle_it 2.572 r_angle_refined_deg 1.856 r_mcbond_it 1.628 r_nbtor_refined 0.275 r_symmetry_hbond_refined 0.235 r_symmetry_vdw_refined 0.196 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 804 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 177
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction