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Crystal structure of Vibrio alkaline phosphatase with bound HEPES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 23% PEG3350, 0.4 M NaCl and 0.1 M HEPES pH 7.5, 10 mg/mL protein. Crystal dehydrated in the mother liquior with PEG3350 increased to 30% prior to data collection
Crystal Properties Matthews coefficient Solvent content 1.51 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.81 α = 90 b = 85.05 β = 113.904 c = 85.5 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 2019-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.918 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.7 44.1 79.6 0.0092 0.998 12.14 5.88 517701 26.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 29.9 1.671 0.375 0.76
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3E2D 1.7 44.1 1.35 88001 2015 79.68 0.151 0.1503 0.1504 0.1812 0.183 33.6
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 14.8462 f_angle_d 0.6541 f_chiral_restr 0.0411 f_plane_restr 0.0037 f_bond_d 0.0036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7804 Nucleic Acid Atoms Solvent Atoms 831 Heterogen Atoms 120
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing