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human O-phosphoethanolamine phospho-lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 20% PEG 3350, 100 mM Bis Tris propane pH 7.0, 200 mM ammonium sulfate, and 3% MPD.
Crystal Properties Matthews coefficient Solvent content 1.93 36.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.998 α = 90 b = 137.998 β = 90 c = 121.87 γ = 120
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 PSI PILATUS 6M 2018-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.05 69.09 99.99 0.068 0.992 10.1 4.9 54318 16.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 0.102
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 5G4I 2.05 69.09 51478 2812 99.96 0.165 0.1631 0.1717 0.1989 0.2077 RANDOM 21
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] 0.44 0.22 0.44 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.593 r_dihedral_angle_3_deg 15.957 r_dihedral_angle_4_deg 15.855 r_dihedral_angle_1_deg 6.761 r_angle_refined_deg 1.605 r_angle_other_deg 1.385 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.593 r_dihedral_angle_3_deg 15.957 r_dihedral_angle_4_deg 15.855 r_dihedral_angle_1_deg 6.761 r_angle_refined_deg 1.605 r_angle_other_deg 1.385 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6296 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PHASER model building SCALA data scaling MOSFLM data processing XDS data reduction PHASER phasing