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Crystal Structure of S. aureus IsdE complexed with heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q8P PDB Entry 2Q8P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 50 mM MES, 0.2M ammonium acetate, 28% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.52 51.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.219 α = 90 b = 64.219 β = 90 c = 144.993 γ = 90
Symmetry Space Group P 43 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 77 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, double crystal monochromator, toroid focusing mirror 2007-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.0 SSRL BL9-2
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 2.15 50 99.7 0.058 21.1 6.3 17270
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 2.15 2.23 99.6 0.363 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 2Q8P 2.15 50 16264 869 99.32 0.20454 0.20207 0.1951 0.25299 0.247 RANDOM 29.675
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] 1.45 1.45 -2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 21.539 r_dihedral_angle_3_deg 16.652 r_dihedral_angle_1_deg 5.715 r_scangle_it 2.315 r_scbond_it 1.546 r_angle_refined_deg 1.304 r_mcangle_it 0.888 r_mcbond_it 0.562 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 21.539 r_dihedral_angle_3_deg 16.652 r_dihedral_angle_1_deg 5.715 r_scangle_it 2.315 r_scbond_it 1.546 r_angle_refined_deg 1.304 r_mcangle_it 0.888 r_mcbond_it 0.562 r_nbtor_refined 0.299 r_nbd_refined 0.186 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.112 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 2076 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 43
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing