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Biochemical studies and crystal structure determination of dihydrodipicolinate synthase from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DHP PDB ENTRY 1DHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG 3350, 170mM MgCl2, 70mM Tris-HCl, 6% propylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.33 47.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.07 α = 90 b = 81.59 β = 90 c = 123.69 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 283 IMAGE PLATE MARRESEARCH Mirror 2009-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.514
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.85 52.57 96.4 14342 14342
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3 98.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1DHP 2.85 52.57 12885 12885 679 94.58 0.20677 0.20498 0.2038 0.2416 0.2439 RANDOM 24.123
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] -0.39 0.56 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.614 r_dihedral_angle_4_deg 22.693 r_dihedral_angle_3_deg 19.337 r_dihedral_angle_1_deg 3.268 r_scangle_it 2.713 r_angle_refined_deg 1.65 r_scbond_it 1.586 r_mcangle_it 1.454 r_mcbond_it 0.762 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.614 r_dihedral_angle_4_deg 22.693 r_dihedral_angle_3_deg 19.337 r_dihedral_angle_1_deg 3.268 r_scangle_it 2.713 r_angle_refined_deg 1.65 r_scbond_it 1.586 r_mcangle_it 1.454 r_mcbond_it 0.762 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4400 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 35
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling