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Crystal structure of the catalytic domain of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ISZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 289 0.2 M Ammonium acetate, 25% PEG 3350, 0.1 M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.667 α = 90 b = 44.721 β = 92.9 c = 92.481 γ = 90
Symmetry Space Group P 1 21 1
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 315r DOUBLE CRYSTAL 2011-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 1.84 40 96.5 0.09 10 2.3 42453 2
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 1.84 1.88 97.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3ISZ 1.84 30 2 42421 40252 2157 95.9 0.197 0.194 0.2044 0.249 0.2572 RANDOM 24.43
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] -1.13 2.51 -1.55 2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.935 r_dihedral_angle_4_deg 19.632 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_1_deg 6.348 r_angle_other_deg 2.95 r_angle_refined_deg 2.035 r_chiral_restr 0.11 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.935 r_dihedral_angle_4_deg 19.632 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_1_deg 6.348 r_angle_other_deg 2.95 r_angle_refined_deg 2.035 r_chiral_restr 0.11 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3799 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 4
Software Software Software Name Purpose SBC-Collect data collection REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing