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1.32 Angstrom Crystal Structure of Ybbr like Domain of lmo2119 Protein from Listeria monocytogenes.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein: 7.2 mg/ml, 0.25M Sodium chloride, 0.1M Tris HCl (pH 8.3);
Screen: Trap96 (D4), 0.2M NAD, 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 1.62 24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.577 α = 90 b = 28.819 β = 95.65 c = 59.733 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 MARMOSAIC 225 mm CCD C(111) 2013-07-25 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 1.32 30 99.8 0.05 0.05 22.9 3.6 18244 -3 14
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 1.32 1.34 99.3 0.512 2.4 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4QDY 1.32 29.72 17262 926 99.84 0.16351 0.16198 0.1923 0.205 RANDOM 16.053
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] 0.32 0.4 -0.58 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.305 r_dihedral_angle_4_deg 15.235 r_dihedral_angle_3_deg 10.391 r_long_range_B_refined 6.676 r_long_range_B_other 5.68 r_dihedral_angle_1_deg 4.114 r_scangle_other 1.892 r_angle_refined_deg 1.561 r_scbond_other 1.206 r_scbond_it 1.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.305 r_dihedral_angle_4_deg 15.235 r_dihedral_angle_3_deg 10.391 r_long_range_B_refined 6.676 r_long_range_B_other 5.68 r_dihedral_angle_1_deg 4.114 r_scangle_other 1.892 r_angle_refined_deg 1.561 r_scbond_other 1.206 r_scbond_it 1.204 r_mcangle_it 1.188 r_mcangle_other 1.187 r_angle_other_deg 0.829 r_mcbond_other 0.743 r_mcbond_it 0.742 r_chiral_restr 0.086 r_gen_planes_refined 0.024 r_gen_planes_other 0.02 r_bond_refined_d 0.012 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 743 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling BALBES phasing