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Dihydrodipicolinate synthase S48W mutant with lysine in the allosteric site, and pyruvate in the catalytic site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXC PDB entry 1YXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294.15 glucopyranoside, potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 3.74 67.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.129 α = 90 b = 121.129 β = 90 c = 111.271 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 294.15 CCD ADSC QUANTUM 315r 2011-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95369 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.82 33.34 100 0.086 0.039 17.5 11 57849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.86 0.329 0.156
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 1YXC 2.07 39.65 54898 2932 99.95 0.17412 0.1723 0.1826 0.20861 0.214 RANDOM 32.966
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.94 r_dihedral_angle_4_deg 19.376 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_1_deg 6.477 r_angle_refined_deg 2.01 r_angle_other_deg 0.951 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.94 r_dihedral_angle_4_deg 19.376 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_1_deg 6.477 r_angle_refined_deg 2.01 r_angle_other_deg 0.951 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 4297 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling PHASER phasing