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Crystal Structure of the sixteen heme cytochrome from Desulfovibrio gigas
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG 8000, zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.889 α = 90 b = 90.799 β = 90 c = 83.934 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2002-10-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.738, 1.744, 1.050 MPG/DESY, HAMBURG BW6
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 2.1 25 96.8 0.039 2.9 40346 2 2
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 2.1 2.17 96.8 0.396 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.1 25 40346 37593 1978 98.16 0.19677 0.195 0.1935 0.2042 0.26029 0.2645 RANDOM 54.494
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] 0.07 0.99 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.225 r_dihedral_angle_4_deg 21.96 r_dihedral_angle_3_deg 18.093 r_sphericity_free 15.051 r_sphericity_bonded 10.391 r_dihedral_angle_1_deg 7.783 r_scangle_it 4.697 r_scbond_it 3.353 r_angle_refined_deg 2.353 r_mcangle_it 2.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.225 r_dihedral_angle_4_deg 21.96 r_dihedral_angle_3_deg 18.093 r_sphericity_free 15.051 r_sphericity_bonded 10.391 r_dihedral_angle_1_deg 7.783 r_scangle_it 4.697 r_scbond_it 3.353 r_angle_refined_deg 2.353 r_mcangle_it 2.144 r_mcbond_it 1.32 r_nbd_refined 0.345 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.281 r_symmetry_vdw_refined 0.28 r_xyhbond_nbd_refined 0.248 r_chiral_restr 0.156 r_metal_ion_refined 0.096 r_bond_refined_d 0.022 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3837 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 749
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHARP phasing