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Structure of siderophore-interacting protein from Vibrio anguillarum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 The crystal of VaSIP was grown in the drop containing 1.4 ul protein solution (60 mg/ml in 10 mM Hepes, 150 mM NaCl, pH 7.5, 1 mM DTT) and 1.4 ul reservoir solution (0.1 M KBr, 30% (W/V) mPEG 2000).
Crystal Properties Matthews coefficient Solvent content 2.03 39.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.622 α = 90 b = 58.466 β = 114.18 c = 70.65 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 PILATUS 6M 2016-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.19 58.951 95.8 0.051 0.055 0.021 0.999 20.2 6.7 147256
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.194 74.6 0.482 0.528 0.21 0.885 3.3 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2gpj 1.19 58.951 1.34 147214 7417 95.76 0.139 0.1378 0.1615 0.1763 14.8159
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 f_dihedral_angle_d 18.394 f_angle_d 1.032 f_chiral_restr 0.081 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3877 Nucleic Acid Atoms Solvent Atoms 607 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing