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2.20 Angstrom resolution crystal structure of protein YE0340 of unidentified function from Yersinia enterocolitica subsp. enterocolitica 8081]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Crystallization: 20%Polyethylene Glycol 8000, 0.2M Sodium Chloride,Phosphate-Citrate
Protein at 20 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.675 α = 87.66 b = 37.135 β = 88.25 c = 82.583 γ = 61.17
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 2015-02-22 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) 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 30 96.1 0.07 16.5 3.7 18325 31
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 2.2 2.24 90 0.337 3.2 3.1
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 1X7V 2.2 29.66 17175 931 96.16 0.23165 0.22883 0.2299 0.28529 0.2877 RANDOM 38.256
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] -18.95 1.75 12.1 -9.65 -6.08 28.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.619 r_dihedral_angle_4_deg 12.121 r_dihedral_angle_3_deg 9.599 r_dihedral_angle_1_deg 2.569 r_angle_refined_deg 1.623 r_angle_other_deg 1.185 r_chiral_restr 0.104 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.619 r_dihedral_angle_4_deg 12.121 r_dihedral_angle_3_deg 9.599 r_dihedral_angle_1_deg 2.569 r_angle_refined_deg 1.623 r_angle_other_deg 1.185 r_chiral_restr 0.104 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.005 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3282 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing