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Crystal structure of Dihydrodipicolinate synthase (TM1521) from Thermotoga maritima at 1.80 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.5 293 28% PEG-400, 0.1M Sodium HEPES pH 7.5, 0.2M Calcium chloride dihydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.672 α = 90 b = 140.768 β = 90 c = 155.943 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 bent conical Si-mirror (Rh coating) 2003-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.61 50 100 0.096 12.18 4.25 68682 68682 30.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.67 65.47 0.712 1.04 1.74 5042
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 1DHP 1.8 35.61 49783 2656 93.33 0.14174 0.13941 0.1537 0.18593 0.1945 RANDOM 25.358
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] 1.84 -0.51 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.241 r_dihedral_angle_4_deg 20.002 r_dihedral_angle_3_deg 13.619 r_scangle_it 7.692 r_dihedral_angle_1_deg 6.139 r_scbond_it 5.534 r_mcangle_it 3.014 r_mcbond_it 2.275 r_angle_refined_deg 1.608 r_angle_other_deg 0.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.241 r_dihedral_angle_4_deg 20.002 r_dihedral_angle_3_deg 13.619 r_scangle_it 7.692 r_dihedral_angle_1_deg 6.139 r_scbond_it 5.534 r_mcangle_it 3.014 r_mcbond_it 2.275 r_angle_refined_deg 1.608 r_angle_other_deg 0.857 r_symmetry_vdw_other 0.342 r_symmetry_hbond_refined 0.248 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.221 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.099 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4539 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement