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Dihydrodipicolinate synthase S48F mutant with lysine in the allosteric site, and pyruvate and succinic semi-aldehyde 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 3.68 66.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.299 α = 90 b = 121.299 β = 90 c = 109.781 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 33.36 100 0.085 0.039 17.6 11 83472
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.86 0.305 0.339
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 1.82 33.36 79236 4166 99.93 0.13752 0.13607 0.1486 0.16512 0.1727 RANDOM 18.222
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.194 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_3_deg 13.469 r_dihedral_angle_1_deg 6.179 r_long_range_B_refined 6.15 r_long_range_B_other 6.15 r_scangle_other 4.685 r_scbond_it 3.212 r_scbond_other 3.212 r_mcangle_other 2.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.194 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_3_deg 13.469 r_dihedral_angle_1_deg 6.179 r_long_range_B_refined 6.15 r_long_range_B_other 6.15 r_scangle_other 4.685 r_scbond_it 3.212 r_scbond_other 3.212 r_mcangle_other 2.487 r_mcangle_it 2.486 r_angle_refined_deg 2.383 r_mcbond_it 1.933 r_mcbond_other 1.932 r_angle_other_deg 1.24 r_chiral_restr 0.159 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4351 Nucleic Acid Atoms Solvent Atoms 682 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling PHASER phasing