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Structure of heme transport protein IsdH-NEAT3 from S. aureus in complex with Manganese(III)-porphyrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 PEG-MME 500 30%, Bicine 0.1M, Sodium Chloride 0.1M, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.28 α = 90 b = 75.93 β = 95.09 c = 49.33 γ = 90
Symmetry Space Group P 1 21 1
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 270 mirror 2010-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 49.14 96.7 0.142 6.6 3.3 8138 8138 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 97 0.404 0.404 0.481 0.258 1.9 3.3 1171
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 2Z6F 2.7 49.14 7754 373 96.61 0.22732 0.22439 0.2279 0.28621 0.293 RANDOM 38.433
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] 3.85 0.39 -1.48 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.964 r_dihedral_angle_4_deg 25.216 r_dihedral_angle_3_deg 17.382 r_dihedral_angle_1_deg 6.702 r_scangle_it 1.449 r_angle_refined_deg 1.23 r_scbond_it 0.842 r_mcangle_it 0.545 r_mcbond_it 0.287 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.964 r_dihedral_angle_4_deg 25.216 r_dihedral_angle_3_deg 17.382 r_dihedral_angle_1_deg 6.702 r_scangle_it 1.449 r_angle_refined_deg 1.23 r_scbond_it 0.842 r_mcangle_it 0.545 r_mcbond_it 0.287 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1816 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 98
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection