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2.35 Angstrom Crystal Structure Minor Lipoprotein from Acinetobacter baumannii.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 15.9 mg/ml, 0.01M Tris HCl (pH 8.3),
Screen: JCSG+ (A8), 0.2M Ammonium formate, 20% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.806 α = 90 b = 68.806 β = 90 c = 96.586 γ = 90
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 MARMOSAIC 300 mm CCD 2016-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.35 30 100 0.058 0.058 31.5 7.5 18791 -3 63.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 99.8 0.723 0.682 2.1 5.5
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 3BF2 2.35 29.32 17811 953 99.88 0.2182 0.21569 0.2161 0.2628 0.2596 RANDOM 70.732
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] 1.58 1.58 -3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.456 r_dihedral_angle_4_deg 10.981 r_dihedral_angle_3_deg 9.085 r_long_range_B_refined 7.174 r_long_range_B_other 7.169 r_scangle_other 4.11 r_mcangle_it 3.974 r_mcangle_other 3.973 r_scbond_it 2.532 r_scbond_other 2.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.456 r_dihedral_angle_4_deg 10.981 r_dihedral_angle_3_deg 9.085 r_long_range_B_refined 7.174 r_long_range_B_other 7.169 r_scangle_other 4.11 r_mcangle_it 3.974 r_mcangle_other 3.973 r_scbond_it 2.532 r_scbond_other 2.531 r_mcbond_it 2.494 r_mcbond_other 2.493 r_dihedral_angle_1_deg 2.276 r_angle_refined_deg 1.463 r_angle_other_deg 0.848 r_chiral_restr 0.081 r_gen_planes_refined 0.021 r_gen_planes_other 0.017 r_bond_refined_d 0.009 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3210 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing