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Structure of a PTP-like phytase from Bdellovibrio bacteriovorus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PSZ PDB entry 2PSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 200 mM MgCl2, 100 mM Tris-HCl (7.0), 8-10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.64 α = 90 b = 78.56 β = 93.13 c = 69.82 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 CCD RAYONIX MX-300 2010-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.698 34.222 99.2 0.078 7.2 3.4 63333 63333 2 1 24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.698 1.79 94.7 0.433 0.433 1.4 3.1 8858
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2PSZ 1.698 34.222 1.5 1.35 63333 63305 3211 99.14 0.1585 0.1581 0.1563 0.1587 0.1928 0.194 Random 31.8236
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 13.962 f_angle_d 1.648 f_chiral_restr 0.086 f_bond_d 0.017 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4241 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 9
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MxDC data collection XDS data reduction PHASER phasing