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Crystal structure of the heme-bound form of the linker-NEAT3 region of IsdH from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VTM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 200mM potassium chloride, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.81 56.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.91 α = 90 b = 95.31 β = 90 c = 99.44 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 ADSC QUANTUM 315 2013-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.8 40.43 97.6 0.082 0.036 0.996 12.3 5.7 43510
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 94.8 0.454 0.217 0.865 2.8
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 3VTM 1.8 40.43 41691 1772 97.07 0.187 0.1854 0.1926 0.2261 0.2327 RANDOM 29.321
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 -1.52 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.859 r_dihedral_angle_4_deg 29.388 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_1_deg 7.47 r_angle_refined_deg 2.015 r_angle_other_deg 1.476 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.859 r_dihedral_angle_4_deg 29.388 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_1_deg 7.47 r_angle_refined_deg 2.015 r_angle_other_deg 1.476 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2958 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing