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Staphylococcus aureus IsdA NEAT domain K75A variant in complex with heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ITF PDB ENTRY 2ITF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 2.0 M ammonium sulfate, 0.1 M citrate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.42 49.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.67 α = 90 b = 76.599 β = 90 c = 35.64 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 CCD ADSC QUANTUM 315r Sample to detector distance: 107 to 650 mm; Maximum vertical offset: 75mm 2010-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.0 SSRL BL7-1
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 1.3 50 97.8 0.06 16 6 34899 14.9
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 1.3 1.35 83.7 0.32 3.1 2924
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 2ITF 1.3 50 34863 1756 97.83 0.1604 0.1591 0.1573 0.1854 0.1841 RANDOM 20.197
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] -0.91 -0.69 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.83 r_dihedral_angle_4_deg 23.878 r_dihedral_angle_3_deg 14.344 r_dihedral_angle_1_deg 6.578 r_scangle_it 5.05 r_scbond_it 3.461 r_mcangle_it 2.697 r_mcbond_it 1.67 r_rigid_bond_restr 1.537 r_angle_refined_deg 1.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.83 r_dihedral_angle_4_deg 23.878 r_dihedral_angle_3_deg 14.344 r_dihedral_angle_1_deg 6.578 r_scangle_it 5.05 r_scbond_it 3.461 r_mcangle_it 2.697 r_mcbond_it 1.67 r_rigid_bond_restr 1.537 r_angle_refined_deg 1.524 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 986 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 49
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling