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Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the PLP-Serine external aldimine state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 292 0.05 M citric acid, 0.05 M BIS-TRIS propane at pH 5.0 and 16% polyethylene glycol 3350 cocrystallized with 50 mM L-serine
Crystal Properties Matthews coefficient Solvent content 3.52 65.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.888 α = 90 b = 93.888 β = 90 c = 134.683 γ = 120
Symmetry Space Group P 31 2 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 2018-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 1.63 44.89 99.9 0.045 1 29.5 11.3 86052 -3
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 1.63 1.73 99.3 1.098 0.847 2.1 11.3
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 6YMD 1.63 44.89 85018 1033 99.86 0.1067 0.1064 0.1081 0.1298 0.129 RANDOM 35.566
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] -0.41 -0.2 -0.41 1.32
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.705 r_dihedral_angle_2_deg 31.849 r_sphericity_bonded 26.156 r_dihedral_angle_4_deg 17.506 r_dihedral_angle_3_deg 13.257 r_dihedral_angle_1_deg 6.301 r_rigid_bond_restr 4.899 r_angle_refined_deg 1.813 r_angle_other_deg 1.168 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.705 r_dihedral_angle_2_deg 31.849 r_sphericity_bonded 26.156 r_dihedral_angle_4_deg 17.506 r_dihedral_angle_3_deg 13.257 r_dihedral_angle_1_deg 6.301 r_rigid_bond_restr 4.899 r_angle_refined_deg 1.813 r_angle_other_deg 1.168 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3207 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing