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Structure of dihydrodipicolinate synthase from Clostridium botulinum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.66 281 Crystal were obtained from a 400 nL drop formed from 200 nL of protein solution (11.2 mg/mL, in 10 mM Tris-HCl, pH 8.0) and 200 nL of precipitant (polyethylene glycol 3350 15.7% w/v, malic acid 100 mM, pH 5.66). The drop was incubated at 281K. The reservoir (80 micro-L) contained polyethylene glycol 3350 (15.7% w/v) and malic acid (100 mM, pH 5.66)., VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.06 40.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.81 α = 90 b = 92.81 β = 90 c = 60.35 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 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 2.23 34.2 94.7 0.046 26.5 6.1 12667
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 2.23 2.35 67.6 0.104 12.5 4.5 1344
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.23 34.2 11388 1250 100 0.14226 0.13492 0.1348 0.20928 0.2091 RANDOM 14.223
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] 0.79 0.79 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.795 r_dihedral_angle_3_deg 13.604 r_dihedral_angle_4_deg 12.232 r_dihedral_angle_1_deg 6.478 r_scangle_it 4.506 r_scbond_it 2.796 r_angle_refined_deg 1.708 r_mcangle_it 1.373 r_mcbond_it 0.767 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.795 r_dihedral_angle_3_deg 13.604 r_dihedral_angle_4_deg 12.232 r_dihedral_angle_1_deg 6.478 r_scangle_it 4.506 r_scbond_it 2.796 r_angle_refined_deg 1.708 r_mcangle_it 1.373 r_mcbond_it 0.767 r_chiral_restr 0.107 r_bond_refined_d 0.021 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 2200 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 24
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling