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X-ray crystal structure of the R336L Vibrio alkaline phosphatase variant.
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, SITTING DROP 8 298 Reservoir conditions 20%(w/v) PEG 3350 and 0.2 M potassium formate.
Protein conditions: 20 mM Tris, 1 mM MgSO4, 5 mM MgCl2, 1.3 mM desthiobiotin, 0.25 M NaCl, 15 % (v/v) ethylene glycol, pH 8.0.
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.082 α = 90 b = 118.596 β = 90 c = 83.922 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS3 S 6M 2016-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2 48.43 100 0.063 0.069 0.027 0.999 20.7 6.6 33403
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.9 0.526 0.569 0.216 0.861 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3E2D 2 48.43 31771 1610 99.93 0.1712 0.1688 0.1787 0.2182 0.222 RANDOM 30.28
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] -0.52 -0.38 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.832 r_dihedral_angle_4_deg 18.006 r_dihedral_angle_3_deg 13.934 r_dihedral_angle_1_deg 6.68 r_angle_refined_deg 1.837 r_angle_other_deg 0.887 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.832 r_dihedral_angle_4_deg 18.006 r_dihedral_angle_3_deg 13.934 r_dihedral_angle_1_deg 6.68 r_angle_refined_deg 1.837 r_angle_other_deg 0.887 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3809 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 23
Software Software Software Name Purpose XDS data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction