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Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the PLP-internal 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
Crystal Properties Matthews coefficient Solvent content 3.54 65.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.383 α = 90 b = 94.383 β = 90 c = 134.466 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 1.77 81.74 99.7 0.092 0.999 15.8 11.3 67717 -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 1.77 1.88 98.1 1.09 0.768 2.2 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 1.77 81.74 66654 1016 99.68 0.1416 0.1411 0.1543 0.1747 0.1776 RANDOM 32.036
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] 0.35 0.17 0.35 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.242 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 12.797 r_dihedral_angle_1_deg 6.142 r_angle_refined_deg 1.702 r_angle_other_deg 1.133 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.242 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 12.797 r_dihedral_angle_1_deg 6.142 r_angle_refined_deg 1.702 r_angle_other_deg 1.133 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3268 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing