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Crystal Structure of the Alkylhydroperoxide Reductase subunit F (AhpF) with NAD+ from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M Na-Hepes, 2.5 % (v/v) PEG 400, 2 M ammonium sulfate, 10 mM cadmium chloride
Crystal Properties Matthews coefficient Solvent content 3.2 61.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.882 α = 90 b = 59.576 β = 111.4 c = 121.508 γ = 90
Symmetry Space Group C 1 2 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 315 mirrors 2014-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00 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 2.4 30 91.9 0.108 6.9 3.7 26052
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 2.4 2.49 90.7 0.648 3.4
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 4O5Q 2.4 27 24472 1317 91.7 0.224 0.221 0.2252 0.285 0.2818 RANDOM 49.03
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] -0.35 0.11 -2.48 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.465 r_dihedral_angle_3_deg 17.496 r_dihedral_angle_4_deg 13.512 r_dihedral_angle_1_deg 7.122 r_mcangle_it 3.848 r_mcbond_it 2.386 r_mcbond_other 2.386 r_angle_refined_deg 1.518 r_angle_other_deg 0.784 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.465 r_dihedral_angle_3_deg 17.496 r_dihedral_angle_4_deg 13.512 r_dihedral_angle_1_deg 7.122 r_mcangle_it 3.848 r_mcbond_it 2.386 r_mcbond_other 2.386 r_angle_refined_deg 1.518 r_angle_other_deg 0.784 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3949 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement DENZO data collection HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction