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Structure of Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F (AhpF) C503A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.1 M Bis-Tris (pH 6.5), 1.5 M ammonium sulfate and 0.1 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 4.37 72.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.101 α = 90 b = 134.101 β = 90 c = 134.101 γ = 90
Symmetry Space Group P 41 3 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 315 2017-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
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 2.5 30 99.7 0.069 22.4 11.2 14035 48.63
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 2.5 2.59 99.7 0.252 7.3 11.7
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 5H29 2.5 30 14035 749 99.67 0.21723 0.21466 0.2198 0.26719 0.264 RANDOM 61.018
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.014 r_dihedral_angle_3_deg 15.656 r_dihedral_angle_4_deg 15.085 r_dihedral_angle_1_deg 5.689 r_long_range_B_refined 4.947 r_long_range_B_other 4.752 r_mcangle_it 2.508 r_mcangle_other 2.507 r_scangle_other 2.004 r_mcbond_it 1.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.014 r_dihedral_angle_3_deg 15.656 r_dihedral_angle_4_deg 15.085 r_dihedral_angle_1_deg 5.689 r_long_range_B_refined 4.947 r_long_range_B_other 4.752 r_mcangle_it 2.508 r_mcangle_other 2.507 r_scangle_other 2.004 r_mcbond_it 1.396 r_mcbond_other 1.394 r_angle_refined_deg 1.088 r_scbond_it 1.069 r_scbond_other 1.065 r_angle_other_deg 0.839 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1611 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing