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Siderophore hydrolase EstB from Aspergillus fumigatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M citrate pH 5.5
0.95 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.53 α = 90 b = 89.66 β = 90 c = 130.09 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 PIXEL DECTRIS EIGER X 16M 2016-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.7 45 98.1 0.057 14.5 5.2 69667
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 1.7 1.8 98.4 0.499 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 2QM0 1.7 15 66039 3476 97.99 0.17783 0.17662 0.1865 0.20083 0.2109 RANDOM 30.713
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] 1.15 1.63 -2.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.578 r_sphericity_free 23.03 r_dihedral_angle_4_deg 14.729 r_dihedral_angle_3_deg 10.306 r_sphericity_bonded 9.538 r_dihedral_angle_1_deg 5.057 r_long_range_B_refined 1.847 r_long_range_B_other 1.643 r_scangle_other 1.174 r_mcangle_it 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.578 r_sphericity_free 23.03 r_dihedral_angle_4_deg 14.729 r_dihedral_angle_3_deg 10.306 r_sphericity_bonded 9.538 r_dihedral_angle_1_deg 5.057 r_long_range_B_refined 1.847 r_long_range_B_other 1.643 r_scangle_other 1.174 r_mcangle_it 1.15 r_mcangle_other 1.15 r_angle_refined_deg 1.056 r_rigid_bond_restr 1.018 r_scbond_it 1.002 r_scbond_other 0.995 r_mcbond_it 0.964 r_mcbond_other 0.964 r_angle_other_deg 0.871 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4457 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing