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PpcD, A cytochrome c7 from Geobacter sulfurreducens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 Crystal obtained from Index screen-95 (30% PEG monomethylether 2000, 0.1 M potassium thiocyanate), pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.4 α = 90 b = 55.9 β = 90 c = 94.8 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 CUSTOM-MADE 2003-08-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.74041, 1.73818, 1.78832, 1.69077, 1.0332 APS 19-BM
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 1.34 50 97 0.047 42.1 4 60576 60576
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) 1.34 1.39 79 0.147 8.4 3 4902
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 (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 1.35 36.04 28548 3111 98.86 0.15171 0.14939 0.1632 0.17256 0.1833 RANDOM 8.874
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] -0.36 0.43 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.232 r_sphericity_free 2.572 r_scangle_it 2.362 r_scbond_it 1.696 r_mcangle_it 1.462 r_angle_refined_deg 1.413 r_sphericity_bonded 1.413 r_rigid_bond_restr 0.98 r_mcbond_it 0.891 r_angle_other_deg 0.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.232 r_sphericity_free 2.572 r_scangle_it 2.362 r_scbond_it 1.696 r_mcangle_it 1.462 r_angle_refined_deg 1.413 r_sphericity_bonded 1.413 r_rigid_bond_restr 0.98 r_mcbond_it 0.891 r_angle_other_deg 0.865 r_nbd_refined 0.428 r_symmetry_vdw_other 0.246 r_nbd_other 0.244 r_xyhbond_nbd_refined 0.176 r_symmetry_vdw_refined 0.149 r_symmetry_hbond_refined 0.128 r_nbtor_other 0.083 r_chiral_restr 0.081 r_gen_planes_other 0.018 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1005 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing