☰ Navigation Tabs
Crystal structure of mono-zinc form of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 291 Ammonium sulfate, 0.2 M NaCl,
0.1 M Na Acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.37 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.176 α = 90 b = 95.709 β = 90 c = 181.179 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 mirrors 2009-06-27 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 30 99.9 0.08 18.7 4.2 54220 54213 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 2.03 100 0.72 2 4.1
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 (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 3IC1 2 28.86 54135 51378 2753 99.87 0.20469 0.20207 0.2063 0.25444 0.2576 RANDOM 26.049
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 -0.24 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.049 r_dihedral_angle_4_deg 17.372 r_dihedral_angle_3_deg 15.255 r_dihedral_angle_1_deg 6.483 r_scangle_it 4.392 r_scbond_it 2.694 r_mcangle_it 1.678 r_angle_refined_deg 1.567 r_angle_other_deg 0.93 r_mcbond_it 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.049 r_dihedral_angle_4_deg 17.372 r_dihedral_angle_3_deg 15.255 r_dihedral_angle_1_deg 6.483 r_scangle_it 4.392 r_scbond_it 2.694 r_mcangle_it 1.678 r_angle_refined_deg 1.567 r_angle_other_deg 0.93 r_mcbond_it 0.924 r_mcbond_other 0.232 r_chiral_restr 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 5671 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 12
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing ARP/wARP model building Coot model building REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling