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Dihydrodipicolinate synthase mutant S48F 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 3.71 66.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.189 α = 90 b = 121.189 β = 90 c = 110.162 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) 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 17.5 11 83589
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 1.82 1.86 0.329
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 33.34 79356 4171 99.93 0.13841 0.13678 0.1514 0.16888 0.1818 RANDOM 18.495
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 34.293 r_dihedral_angle_4_deg 17.474 r_dihedral_angle_3_deg 13.068 r_dihedral_angle_1_deg 6.305 r_long_range_B_refined 5.713 r_long_range_B_other 5.711 r_scangle_other 4.517 r_scbond_it 3.127 r_scbond_other 3.127 r_mcangle_other 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.293 r_dihedral_angle_4_deg 17.474 r_dihedral_angle_3_deg 13.068 r_dihedral_angle_1_deg 6.305 r_long_range_B_refined 5.713 r_long_range_B_other 5.711 r_scangle_other 4.517 r_scbond_it 3.127 r_scbond_other 3.127 r_mcangle_other 2.47 r_mcangle_it 2.469 r_angle_refined_deg 2.283 r_mcbond_it 1.932 r_mcbond_other 1.931 r_angle_other_deg 1.212 r_chiral_restr 0.163 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 4333 Nucleic Acid Atoms Solvent Atoms 736 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling PHASER phasing