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X-ray structure of Pen from Bacillus thuringiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 2.2-2.5 M ammonium sulfate, 100 mM HEPES, 5 mM UDP-GlcNAc
Crystal Properties Matthews coefficient Solvent content 2.57 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.524 α = 90 b = 141.876 β = 111.66 c = 93.244 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 Bruker Platinum 135 2016-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 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 2.7 86.66 90.7 0.094 0.094 9.8 5 55673
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 2.7 2.8 84.1 0.301 0.301 2.4 2.2
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 2gn4 2.7 30 52775 2896 90.68 0.20395 0.20133 0.2058 0.2512 0.2558 RANDOM 26.501
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] -1.72 -0.92 3.28 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.517 r_dihedral_angle_3_deg 20.374 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_1_deg 7.572 r_long_range_B_refined 4.033 r_long_range_B_other 4.008 r_mcangle_it 2.384 r_mcangle_other 2.384 r_scangle_other 2.218 r_angle_refined_deg 1.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.517 r_dihedral_angle_3_deg 20.374 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_1_deg 7.572 r_long_range_B_refined 4.033 r_long_range_B_other 4.008 r_mcangle_it 2.384 r_mcangle_other 2.384 r_scangle_other 2.218 r_angle_refined_deg 1.733 r_mcbond_it 1.399 r_mcbond_other 1.399 r_scbond_it 1.283 r_scbond_other 1.275 r_angle_other_deg 0.998 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15321 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 547
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing