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Crystal structure of PtmB in complex with cyclo-(L-Trp-L-Trp) and Adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M Bis-Tris pH 5.5
0.2M Ammonium acetate
25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.453 α = 90 b = 84.453 β = 90 c = 133.377 γ = 90
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 2023-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
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 2.6 25.01 99.87 0.1549 0.998 17.29 13.7 28724
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.693 100 0.851 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.6 25.01 28724 1439 99.87 0.17102 0.2064 0.2071 0.2569 0.2556 RANDOM 40.63
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] 0.73 0.73 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.552 r_dihedral_angle_4_deg 18.462 r_dihedral_angle_3_deg 17.057 r_long_range_B_other 8.645 r_long_range_B_refined 8.636 r_dihedral_angle_1_deg 7.35 r_scangle_other 6.04 r_mcangle_it 5.954 r_mcangle_other 5.953 r_scbond_it 3.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.552 r_dihedral_angle_4_deg 18.462 r_dihedral_angle_3_deg 17.057 r_long_range_B_other 8.645 r_long_range_B_refined 8.636 r_dihedral_angle_1_deg 7.35 r_scangle_other 6.04 r_mcangle_it 5.954 r_mcangle_other 5.953 r_scbond_it 3.958 r_scbond_other 3.957 r_mcbond_it 3.882 r_mcbond_other 3.882 r_angle_refined_deg 1.637 r_angle_other_deg 1.288 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 5916 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling PHASER phasing XDS data reduction