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Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 291 0.2 M NaCl,
0.1 M NaAcetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.697 α = 90 b = 95.751 β = 90 c = 185.426 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 315 double crystal 2009-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 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 2.3 40 95.9 0.086 17.8 4.8 36163 34773 2 2
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 2.3 2.34 99.7 0.57 3.1 4.8
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 1VGY 2.3 40 2 34621 33237 1384 95.7 0.195 0.194 0.2053 0.25 0.2024 RANDOM 32.94
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] 0.35 1.22 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.083 r_dihedral_angle_4_deg 19.568 r_dihedral_angle_3_deg 15.229 r_dihedral_angle_1_deg 6.409 r_scangle_it 3.384 r_scbond_it 2.078 r_angle_refined_deg 1.429 r_mcangle_it 1.34 r_angle_other_deg 0.907 r_mcbond_it 0.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.083 r_dihedral_angle_4_deg 19.568 r_dihedral_angle_3_deg 15.229 r_dihedral_angle_1_deg 6.409 r_scangle_it 3.384 r_scbond_it 2.078 r_angle_refined_deg 1.429 r_mcangle_it 1.34 r_angle_other_deg 0.907 r_mcbond_it 0.704 r_mcbond_other 0.137 r_chiral_restr 0.08 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5695 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 41
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling