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Human methemoglobin in complex with the second and third NEAT domains of IsdH(F365Y/A369F/Y642A) from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.2 M K/Na tartrate, 0.1 M tri-sodium citrate pH 5.6, 2 M ammonium sulfate. Cryoprotected in 20% glycerol.
Crystal Properties Matthews coefficient Solvent content 3.2 61.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.219 α = 90 b = 92.219 β = 90 c = 365.116 γ = 120
Symmetry Space Group P 65 2 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 210r 2013-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.96580 Australian Synchrotron MX1
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 2.55 33.39 99.9 0.138 0.042 0.996 9.3 9.6 31237
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 2.55 2.66 100 0.825 0.252 0.766 2 9.7 3709
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 4IJ2 2.55 33.39 29544 1581 99.72 0.2608 0.2594 0.2598 0.2871 0.2865 RANDOM 67.181
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] 0.79 0.4 0.79 -2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.127 r_dihedral_angle_4_deg 12.169 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 4.735 r_mcangle_it 2.32 r_mcbond_other 1.368 r_mcbond_it 1.367 r_angle_refined_deg 0.789 r_angle_other_deg 0.642 r_chiral_restr 0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.127 r_dihedral_angle_4_deg 12.169 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 4.735 r_mcangle_it 2.32 r_mcbond_other 1.368 r_mcbond_it 1.367 r_angle_refined_deg 0.789 r_angle_other_deg 0.642 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4771 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction iMOSFLM data reduction