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Bicyclic peptide bp70 in I4132 at 1.0 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.2 M CALCIUM CHLORIDE DIHYDRATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 20% V/V 2-PROPANOL
Crystal Properties Matthews coefficient Solvent content 2.09 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.459 α = 90 b = 55.459 β = 90 c = 55.459 γ = 90
Symmetry Space Group I 41 3 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 PILATUS 2M-F COLLIMATING MIRROR (M1), BARTELS MONOCHROMATOR (DCCM), TOROIDAL MIRROR (M2) 2019-02-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000036 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.04 39.24 99.92 0.047 0.045 0.006 1 51.2 65 7245
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.04 1.06 98.58 2.927 1 19.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 FREE R-VALUE 6Y13 1.04 39.24 7230 7230 99.92 0.4391 0.2345 0.4217 RANDOM 25.4355
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]
RMS Deviations Key Refinement Restraint Deviation s_angle_d 0.514 s_non_zero_chiral_vol 0.318 s_zero_chiral_vol 0.132 s_similar_adp_cmpnt 0.084 s_anti_bump_dis_restr 0.039 s_bond_d 0.025 s_from_restr_planes 0.006 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 105 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SHELX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction