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Crystal structure of beta-alanine synthase from Saccharomyces kluyveri in complex with the product beta-alanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R43 PDB ENTRY 1R43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.75 PEG 6000, TRIS PH 8.5, BICINE PH 9.0, LICL.
Crystal Properties Matthews coefficient Solvent content 2.08 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.1 α = 90 b = 217.3 β = 91.9 c = 81.6 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC CCD 2007-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 20 99.6 0.16 7.4 4.9 59732 2
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 2.5 2.6 99.8 0.35 5.29 4.9
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 PDB ENTRY 1R43 2.5 19.84 56799 2931 99.8 0.191 0.189 0.1903 0.231 0.2333 RANDOM 26.36
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] 0.84 -1.19 -1.64 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.343 r_dihedral_angle_4_deg 18.849 r_dihedral_angle_3_deg 17.108 r_dihedral_angle_1_deg 5.567 r_scangle_it 1.761 r_angle_refined_deg 1.174 r_scbond_it 1.086 r_mcangle_it 0.59 r_mcbond_it 0.343 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.343 r_dihedral_angle_4_deg 18.849 r_dihedral_angle_3_deg 17.108 r_dihedral_angle_1_deg 5.567 r_scangle_it 1.761 r_angle_refined_deg 1.174 r_scbond_it 1.086 r_mcangle_it 0.59 r_mcbond_it 0.343 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13396 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing