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Siderophore hydrolase EstB from Aspergillus nidulans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GUD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES pH 7.0
20 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.28 46.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.46 α = 90 b = 72.05 β = 111.97 c = 108.1 γ = 90
Symmetry Space Group P 1 21 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 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 2 45 97.1 0.054 10 3 82011
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 2.1 98.4 0.581 1.7
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 6GUD 2 15 77699 4089 96.93 0.19696 0.19498 0.2028 0.23429 0.2416 RANDOM 50.114
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] -1.66 -0.85 0.97 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.225 r_sphericity_free 27.347 r_sphericity_bonded 25.229 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_3_deg 13.583 r_dihedral_angle_1_deg 5.612 r_long_range_B_refined 2.323 r_long_range_B_other 2.189 r_mcangle_it 1.279 r_mcangle_other 1.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.225 r_sphericity_free 27.347 r_sphericity_bonded 25.229 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_3_deg 13.583 r_dihedral_angle_1_deg 5.612 r_long_range_B_refined 2.323 r_long_range_B_other 2.189 r_mcangle_it 1.279 r_mcangle_other 1.279 r_scangle_other 1.019 r_mcbond_it 0.859 r_mcbond_other 0.859 r_angle_refined_deg 0.761 r_scbond_it 0.707 r_scbond_other 0.707 r_angle_other_deg 0.685 r_rigid_bond_restr 0.172 r_chiral_restr 0.033 r_bond_refined_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9312 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing