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Crystal structure of YetJ from Bacillus Subtilis crystallized in lipidic cubic phase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8 298 0.1 M Tris, pH 7.8, 5% PGA-LM (w/v), and 30% PEG 400 (v/v)
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.864 α = 90 b = 63.037 β = 93.95 c = 47.336 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 PIXEL DECTRIS PILATUS 6M 2016-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 47.22 95.3 6 7 6634
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.63
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 4PGR 2.5 47.22 6273 343 95.04 0.24347 0.24258 0.2445 0.26025 0.2633 RANDOM 38.99
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] 1.06 -1.28 1.37 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.771 r_dihedral_angle_4_deg 16.207 r_dihedral_angle_3_deg 14.147 r_dihedral_angle_1_deg 3.998 r_long_range_B_refined 3.446 r_long_range_B_other 3.399 r_mcangle_it 1.775 r_mcangle_other 1.774 r_scangle_other 1.731 r_scbond_it 1.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.771 r_dihedral_angle_4_deg 16.207 r_dihedral_angle_3_deg 14.147 r_dihedral_angle_1_deg 3.998 r_long_range_B_refined 3.446 r_long_range_B_other 3.399 r_mcangle_it 1.775 r_mcangle_other 1.774 r_scangle_other 1.731 r_scbond_it 1.028 r_scbond_other 1.027 r_mcbond_it 1.022 r_mcbond_other 1.021 r_angle_refined_deg 0.986 r_angle_other_deg 0.883 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 1592 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing