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Structure of LpxD from Acinetobacter baumannii at 2.66A resolution (P4322 form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 2ul of 12mg/ml protein, 2ul of 19% PEG3350, 0.4M magnesium acetate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.667 α = 90 b = 64.667 β = 90 c = 463.814 γ = 90
Symmetry Space Group P 43 2 2
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 RAYONIX MX-300 2011-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9794 APS 21-ID-D
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 2.66 50 99.2 0.12 16.9 9.1 29759 29759 -4
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 2.66 2.76 100 0.572 4.2 9.5 2889
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 4E75 2.66 49.6 28213 1508 0.23708 0.23367 0.2266 0.29973 0.292 RANDOM 42.952
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] 1.09 1.09 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.02 r_dihedral_angle_4_deg 19.237 r_dihedral_angle_3_deg 18.56 r_dihedral_angle_1_deg 6.515 r_scangle_it 2.386 r_scbond_it 1.431 r_angle_refined_deg 1.352 r_mcangle_it 1.217 r_mcbond_it 0.669 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.02 r_dihedral_angle_4_deg 19.237 r_dihedral_angle_3_deg 18.56 r_dihedral_angle_1_deg 6.515 r_scangle_it 2.386 r_scbond_it 1.431 r_angle_refined_deg 1.352 r_mcangle_it 1.217 r_mcbond_it 0.669 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 7709 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling