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Murine pyridoxal phosphatase in complex with 7,8-dihydroxyflavone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 295 Protein solution:
10 mg/ml protein in 50 mM triethanolamine, 250 mM NaCl and 5 mM MgCl2 at pH 7.4 with 3-fold molar excess of 7,8-DHF
Reservoir solution
0.1 M phosphate-citrate buffer and 40% v/v PEG 300
Crystal Properties Matthews coefficient Solvent content 3.08 60.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.011 α = 90 b = 167.011 β = 90 c = 167.011 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 2020-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 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 50 99.8 0.19 0.192 0.03 1 20.66 41 52033 39.35
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 2.12 98.7 3.667 3.713 0.772 0.516 1.21 40.66
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 44.64 1.34 51995 2545 99.88 0.1856 0.1844 0.1834 0.2094 0.2091 50.19
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 14.1596 f_angle_d 0.5307 f_chiral_restr 0.0387 f_plane_restr 0.0078 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4379 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing