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Racemic structure of the cyclic plant peptide PDP-23
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 Crystals were obtained from a racemic mix of 7mg/ml each of L- and D-peptide in 0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% PEG monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 1.58 22.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.527 α = 90 b = 49.008 β = 92.284 c = 29.402 γ = 90
Symmetry Space Group P 1 21/n 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 EIGER X 16M 2020-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.46 49.01 98.8 0.998 10.6 6.4 13346
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 1.46 1.49 80.8 0.833 2.5 6.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7L51 1.464 25.198 13041 619 98.691 0.192 0.1881 0.1947 0.2763 0.2911 20.907
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] -1.867 -0.719 -2.209 4.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_3_deg 10.299 r_rigid_bond_restr 8.917 r_dihedral_angle_1_deg 8.137 r_scangle_it 5.811 r_scangle_other 5.669 r_lrange_other 5.145 r_lrange_it 5.129 r_scbond_it 5.108 r_scbond_other 4.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_3_deg 10.299 r_rigid_bond_restr 8.917 r_dihedral_angle_1_deg 8.137 r_scangle_it 5.811 r_scangle_other 5.669 r_lrange_other 5.145 r_lrange_it 5.129 r_scbond_it 5.108 r_scbond_other 4.999 r_mcangle_it 3.858 r_mcangle_other 3.854 r_mcbond_it 3.263 r_mcbond_other 3.251 r_angle_refined_deg 1.822 r_angle_other_deg 1.664 r_nbd_other 0.283 r_symmetry_nbd_refined 0.263 r_nbd_refined 0.221 r_nbtor_refined 0.2 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.191 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.111 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 438 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing