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Crystal structure of alkaline phosphatase PafA T79S, N100A, K162A, R164A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 291 22% PEG3350, 0.1 M sodium acetate, pH 4.4, 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.95 32.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.329 α = 90 b = 113.329 β = 90 c = 69.79 γ = 90
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 2016-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.03 41.01 99.9 0.168 0.995 9.6 8.5 28568 30.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.08 99.9 1.518 0.66 8.8
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 FREE R-VALUE 5TJ3 2.031 41.009 1.35 28561 1493 99.79 0.1724 0.1704 0.2086 0.2167 40.6973
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 19.638 f_angle_d 1.184 f_chiral_restr 0.069 f_bond_d 0.013 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4019 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 5
Software Software Software Name Purpose Blu-Ice data collection Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction Coot model building