☰ Navigation Tabs
Crystal Structure of Dihydrodipicolinate Synthase DapA-2 (BA3935) from Bacillus Anthracis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 PEG 3350, NaFormate, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.9 57.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.463 α = 90 b = 126.564 β = 90 c = 134.636 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 100 CCD ADSC QUANTUM 4 Mirror 2004-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.97600 SRS PX14.2
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 50 99.8 0.117 25.13 6.1 74365 74365
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) 2.23 2.31 99.1 0.51 5.49 4.5 7299
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 (All) 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 1XKY 2.23 46.13 67750 67750 3609 100 0.1972 0.1972 0.19408 0.2025 0.25432 0.2595 RANDOM 40.581
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] 0.3 0.25 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.047 r_dihedral_angle_4_deg 18.602 r_dihedral_angle_3_deg 18.555 r_dihedral_angle_1_deg 6.752 r_scangle_it 3.267 r_scbond_it 2.093 r_angle_refined_deg 1.69 r_mcangle_it 1.201 r_mcbond_it 1.014 r_angle_other_deg 0.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.047 r_dihedral_angle_4_deg 18.602 r_dihedral_angle_3_deg 18.555 r_dihedral_angle_1_deg 6.752 r_scangle_it 3.267 r_scbond_it 2.093 r_angle_refined_deg 1.69 r_mcangle_it 1.201 r_mcbond_it 1.014 r_angle_other_deg 0.917 r_symmetry_vdw_other 0.275 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.192 r_nbd_other 0.179 r_mcbond_other 0.174 r_nbtor_refined 0.172 r_symmetry_hbond_refined 0.149 r_symmetry_vdw_refined 0.128 r_chiral_restr 0.097 r_nbtor_other 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8776 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing