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YaxB from Yersinia enterocolitica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.2 M Na/K-phosphate
Crystal Properties Matthews coefficient Solvent content 5.37 77.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.7 α = 90 b = 111.7 β = 90 c = 169.66 γ = 120
Symmetry Space Group P 65 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 PIXEL DECTRIS EIGER X 16M 2015-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 4 50 98.7 0.069 0.999 13 5 5633
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 4 4.1 99.2 0.958 0.73 2.1
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 6EK4 4 48.82 5351 282 98.65 0.32625 0.32555 0.3202 0.33881 0.3362 RANDOM 196.051
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] 6.23 3.11 6.23 -20.2
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 78.001 r_dihedral_angle_2_deg 39.936 r_dihedral_angle_3_deg 17.341 r_dihedral_angle_4_deg 11.518 r_long_range_B_refined 8.348 r_long_range_B_other 8.347 r_scangle_other 5.987 r_mcangle_it 5.714 r_mcangle_other 5.713 r_dihedral_angle_1_deg 4.623
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 78.001 r_dihedral_angle_2_deg 39.936 r_dihedral_angle_3_deg 17.341 r_dihedral_angle_4_deg 11.518 r_long_range_B_refined 8.348 r_long_range_B_other 8.347 r_scangle_other 5.987 r_mcangle_it 5.714 r_mcangle_other 5.713 r_dihedral_angle_1_deg 4.623 r_mcbond_other 4.249 r_mcbond_it 4.248 r_scbond_it 3.989 r_scbond_other 3.987 r_rigid_bond_restr 1.74 r_angle_other_deg 0.991 r_angle_refined_deg 0.904 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing