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P21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Identical protein in P212121 spacegroup
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 ammonium sulphate, bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.69 α = 90 b = 34.005 β = 110.49 c = 108.313 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 ADSC QUANTUM 4 2000-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 0.9 ESRF ID13
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 1.55 15 92.1 91758 84418
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.55 1.59 90
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 Identical protein in P212121 spacegroup 1.55 14.92 91750 84418 4456 0.17458 0.1745 0.17265 0.1751 0.21148 0.2267 RANDOM 20.014
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] 0.13 -0.44 -0.12 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.398 r_dihedral_angle_1_deg 6.08 r_scangle_it 3.297 r_scbond_it 2.239 r_angle_refined_deg 1.573 r_mcangle_it 1.567 r_mcbond_it 0.889 r_nbd_refined 0.357 r_symmetry_vdw_refined 0.333 r_symmetry_hbond_refined 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.398 r_dihedral_angle_1_deg 6.08 r_scangle_it 3.297 r_scbond_it 2.239 r_angle_refined_deg 1.573 r_mcangle_it 1.567 r_mcbond_it 0.889 r_nbd_refined 0.357 r_symmetry_vdw_refined 0.333 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.108 r_xyhbond_nbd_refined 0.108 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3750 Nucleic Acid Atoms Solvent Atoms 1161 Heterogen Atoms 1052
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement