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Crystal structure of DNA-binding domain of OmpR of two-component system of Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 Bistris propane, Na2SO4, PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.62 53.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.47 α = 90.07 b = 49.703 β = 99.01 c = 52.727 γ = 103.98
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2017-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.2 48.2 98.1 0.15 0.99 6.1 3.6 23437
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 2.2 2.3 97.3 0.85 0.74 3.7
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 1OPC 2.2 48.2 22272 1164 98.08 0.24344 0.24196 0.253 0.27297 0.285 RANDOM 32.525
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] 4.26 1.08 -0.08 -2.86 0.49 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.094 r_dihedral_angle_4_deg 15.038 r_dihedral_angle_3_deg 14.161 r_long_range_B_refined 7.414 r_long_range_B_other 7.412 r_dihedral_angle_1_deg 6.755 r_scangle_other 5.456 r_mcangle_other 4.1 r_mcangle_it 4.099 r_scbond_it 3.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.094 r_dihedral_angle_4_deg 15.038 r_dihedral_angle_3_deg 14.161 r_long_range_B_refined 7.414 r_long_range_B_other 7.412 r_dihedral_angle_1_deg 6.755 r_scangle_other 5.456 r_mcangle_other 4.1 r_mcangle_it 4.099 r_scbond_it 3.507 r_scbond_other 3.506 r_mcbond_it 2.691 r_mcbond_other 2.673 r_angle_refined_deg 1.581 r_angle_other_deg 1.244 r_chiral_restr 0.066 r_bond_refined_d 0.009 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3245 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing