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Crystal structure of an isatin hydrolase bound to product analogue thioisatinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J0N PDB ENTRY 4J0N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 16% w/V PEG3350, 0.2 M calcium acetate, 1 mM MnCl2, 1 mM thioisatin (Benzo[b]thiophene-2,3-dione), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.98 α = 90 b = 51.82 β = 91.92 c = 357.09 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 PSI PILATUS 6M 2013-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.2395 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.9 49.506 98 0.11 8.53 3.9 471486 2 2
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 1.9 2 96.5 0.53 2.83 3.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4J0N 1.9 29.976 1.99 291160 471287 23591 98.21 0.154 0.152 0.1539 0.1923 0.1933
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 12.679 f_angle_d 1.062 f_chiral_restr 0.046 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23679 Nucleic Acid Atoms Solvent Atoms 3329 Heterogen Atoms 172
Software Software Software Name Purpose MxCuBE data collection PHENIX model building PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing