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Crystal structure of mutant E159A of beta-alanine synthase from Saccharomyces kluyveri
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 VAPOR DIFFUSION, HANGING DROP 6 293 TRISODIUM CITRATE, DIOXANE, ACETONE, DTT, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.45 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.117 α = 90 b = 77.143 β = 97.12 c = 108.228 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 2006-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.3 50 97 0.08 11.9 3.2 43156 2 48.8
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 2.3 2.4 88 0.46 2 2.7
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 2.3 45.22 40838 2195 96.6 0.232 0.23 0.2304 0.276 0.2738 RANDOM 27.42
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] 3.8 2.99 -2.61 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.168 r_dihedral_angle_4_deg 18.353 r_dihedral_angle_3_deg 16.715 r_dihedral_angle_1_deg 5.698 r_scangle_it 1.616 r_angle_refined_deg 1.131 r_scbond_it 1.066 r_mcangle_it 0.63 r_mcbond_it 0.368 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.168 r_dihedral_angle_4_deg 18.353 r_dihedral_angle_3_deg 16.715 r_dihedral_angle_1_deg 5.698 r_scangle_it 1.616 r_angle_refined_deg 1.131 r_scbond_it 1.066 r_mcangle_it 0.63 r_mcbond_it 0.368 r_nbtor_refined 0.298 r_xyhbond_nbd_refined 0.291 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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 6679 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing