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The Crystal Structure of RraA from PAO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q5X PDB ENTRY 1Q5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 100mM Tris-HCl pH 8.5, 30% (v/v) PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.64 66.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.679 α = 90 b = 98.679 β = 90 c = 180.26 γ = 120
Symmetry Space Group P 63 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2007-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU RU200 1.5418
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 1.9 50 95 0.0653 0.0632 11.2 8 39611 39040 2 1 35.735
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 94.9 0.245 0.45 8 7.2 39040
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 PDB ENTRY 1Q5X 1.9 30 37561 2007 95.21 0.22222 0.22081 0.2165 0.24898 0.2426 RANDOM 30.542
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] 0.16 0.08 0.16 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.478 r_dihedral_angle_4_deg 18.629 r_dihedral_angle_3_deg 14.129 r_dihedral_angle_1_deg 5.443 r_scangle_it 1.082 r_angle_refined_deg 0.986 r_scbond_it 0.644 r_mcangle_it 0.396 r_nbtor_refined 0.299 r_mcbond_it 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.478 r_dihedral_angle_4_deg 18.629 r_dihedral_angle_3_deg 14.129 r_dihedral_angle_1_deg 5.443 r_scangle_it 1.082 r_angle_refined_deg 0.986 r_scbond_it 0.644 r_mcangle_it 0.396 r_nbtor_refined 0.299 r_mcbond_it 0.22 r_nbd_refined 0.168 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.09 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2416 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 294
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection AUTOMAR data reduction AMoRE phasing