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Crystal structure of octaheme cytochrome c from Shewanella oneidensis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.1M sodium cacodylate, 0.2M KSCN, 25% PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.34 47.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.59 α = 90 b = 61.767 β = 90 c = 185.237 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 100 CCD MARRESEARCH 2002-09-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.7377, 1.7389, 1.6980 EMBL/DESY, HAMBURG BW7A
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 23.8 96.6 0.063 21.53 24585 23745 38
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 93.7 0.354 4.18 2253
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.2 23.77 22479 1217 100 0.181 0.15983 0.15504 0.1585 0.25231 0.249 RANDOM 37.953
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] 2.32 -1.15 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.124 r_scangle_it 5.595 r_scbond_it 3.913 r_mcangle_it 2.392 r_angle_refined_deg 2.287 r_mcbond_it 1.359 r_symmetry_hbond_refined 0.367 r_nbd_refined 0.314 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.124 r_scangle_it 5.595 r_scbond_it 3.913 r_mcangle_it 2.392 r_angle_refined_deg 2.287 r_mcbond_it 1.359 r_symmetry_hbond_refined 0.367 r_nbd_refined 0.314 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.167 r_metal_ion_refined 0.043 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3426 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 347
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing