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Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XYC 1XYC, with residue 44 in each chain removed.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 280 Drops contained: protein solution (~5 mg mL-1 in Tris.HCl 20 mM, pH 8, 2.5 uL), precipitant (K2HPO4 1.8 M, pH 10, 1.2 uL), and N-octyl-beta-R-glucopyranoside (6% w/v, 0.6 uL). Crystals appeared after 3-5 days and grew to dimensions of up to 0.2 mm., VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 3.71 66.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.04 α = 90 b = 121.04 β = 90 c = 110.319 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 110 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.7 33.31 99.2 0.054 12.6 4.1 101750 3
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 1.7 1.76 100 0.38 3 3.91
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 1XYC, with residue 44 in each chain removed. 1.7 33.31 96628 5100 100 0.18049 0.1791 0.1904 0.20733 0.2163 RANDOM, THIN SHELL 22.34
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] -0.43 -0.22 -0.43 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.573 r_dihedral_angle_4_deg 19.244 r_dihedral_angle_3_deg 12.138 r_dihedral_angle_1_deg 6.107 r_scangle_it 3.853 r_scbond_it 2.274 r_angle_refined_deg 1.469 r_mcangle_it 1.277 r_angle_other_deg 0.98 r_mcbond_it 0.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.573 r_dihedral_angle_4_deg 19.244 r_dihedral_angle_3_deg 12.138 r_dihedral_angle_1_deg 6.107 r_scangle_it 3.853 r_scbond_it 2.274 r_angle_refined_deg 1.469 r_mcangle_it 1.277 r_angle_other_deg 0.98 r_mcbond_it 0.705 r_symmetry_vdw_other 0.275 r_nbd_refined 0.237 r_mcbond_other 0.21 r_nbd_other 0.199 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.163 r_symmetry_vdw_refined 0.131 r_metal_ion_refined 0.111 r_symmetry_hbond_refined 0.096 r_chiral_restr 0.089 r_nbtor_other 0.087 r_xyhbond_nbd_other 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other 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 711 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling AMoRE phasing