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Crystal structure of heme binding protein HmuT H141A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 2.25 M Ammonium sulfate, 0.20 M Potassium thiocyanate, 0.20 M Ammonium tartrate, 5%(v/v) Polypropylene glycol, 0.025%(w/v) beta-Octyl glucoside
Crystal Properties Matthews coefficient Solvent content 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.38 α = 90 b = 73.38 β = 90 c = 147.42 γ = 90
Symmetry Space Group P 41 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 RAYONIX MX300HE 2014-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90 SPring-8 BL44XU
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 48.94 98.8 0.058 19.98 9.58 97636
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 1.34 96.6 0.551 3.73
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 5az3 1.3 48.94 92836 4800 98.8 0.15195 0.15106 0.1509 0.16894 0.1685 RANDOM 14.139
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] -0.07 -0.07 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.711 r_sphericity_free 17.901 r_dihedral_angle_4_deg 12.789 r_dihedral_angle_3_deg 10.391 r_dihedral_angle_1_deg 5.819 r_sphericity_bonded 5.202 r_long_range_B_refined 1.894 r_long_range_B_other 1.662 r_angle_refined_deg 1.318 r_scangle_other 1.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.711 r_sphericity_free 17.901 r_dihedral_angle_4_deg 12.789 r_dihedral_angle_3_deg 10.391 r_dihedral_angle_1_deg 5.819 r_sphericity_bonded 5.202 r_long_range_B_refined 1.894 r_long_range_B_other 1.662 r_angle_refined_deg 1.318 r_scangle_other 1.228 r_mcangle_it 1.013 r_mcangle_other 1.013 r_scbond_it 0.985 r_scbond_other 0.98 r_angle_other_deg 0.931 r_mcbond_it 0.728 r_mcbond_other 0.725 r_rigid_bond_restr 0.697 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2239 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing