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Crystal structure of mutant E159A of beta-alanine synthase from Saccharomyces kluyveri in complex with its substrate N-carbamyl-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 2.07 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.78 α = 90 b = 218.3 β = 92.19 c = 81.58 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 2006-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 20 99.5 0.1 9.48 4.1 116114 2 28.4
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 2.1 99.3 0.27 4.84 4.2
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 19.76 110321 5792 99.6 0.18 0.178 0.1811 0.208 0.2115 RANDOM 27.59
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] 3.07 -0.22 -3.35 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.352 r_dihedral_angle_4_deg 17.362 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 5.472 r_scangle_it 1.827 r_scbond_it 1.185 r_angle_refined_deg 1.096 r_mcangle_it 0.592 r_mcbond_it 0.36 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.352 r_dihedral_angle_4_deg 17.362 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 5.472 r_scangle_it 1.827 r_scbond_it 1.185 r_angle_refined_deg 1.096 r_mcangle_it 0.592 r_mcbond_it 0.36 r_nbtor_refined 0.297 r_xyhbond_nbd_refined 0.202 r_nbd_refined 0.181 r_symmetry_hbond_refined 0.177 r_symmetry_vdw_refined 0.154 r_chiral_restr 0.078 r_bond_refined_d 0.009 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 13359 Nucleic Acid Atoms Solvent Atoms 956 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing