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Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with diaminopimelate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M Ammonium tartrate, 15%-20% PEG3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.873 α = 90 b = 98.225 β = 105.51 c = 98.438 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 2009-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.79 94.86 99.14 93970
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3TD3 1.79 94.86 93970 4939 99.14 0.18048 0.17868 0.1784 0.21444 0.2146 RANDOM 17.44
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] -0.43 0.02 0.17 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.767 r_dihedral_angle_3_deg 15.236 r_dihedral_angle_4_deg 13.908 r_scangle_it 7.369 r_dihedral_angle_1_deg 6.563 r_scbond_it 4.657 r_mcangle_it 2.595 r_angle_refined_deg 2.444 r_mcbond_it 1.483 r_chiral_restr 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.767 r_dihedral_angle_3_deg 15.236 r_dihedral_angle_4_deg 13.908 r_scangle_it 7.369 r_dihedral_angle_1_deg 6.563 r_scbond_it 4.657 r_mcangle_it 2.595 r_angle_refined_deg 2.444 r_mcbond_it 1.483 r_chiral_restr 0.217 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 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 7730 Nucleic Acid Atoms Solvent Atoms 623 Heterogen Atoms 104
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling