6Y14

Bicyclic peptide bp65 crystallized as racemic mixture at 0.9 Angstrom resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62910.1 M Sodium citrate tribasic dihydrate pH 5.6, 35% v/v tert-Butanol
Crystal Properties
Matthews coefficientSolvent content
2.8845.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 16.482α = 111.28
b = 26.209β = 92.26
c = 29.909γ = 101.96
Symmetry
Space GroupP -1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2017-12-20MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.8SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
10.927.787.710.1650.2330.1650.9250.2334.51.7629455
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.90.9284.730.2470.3490.2470.8862.21.76

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONAB INITIO PHASINGFREE R-VALUENONE0.927.72945587.70.19130.1264RANDOM3.95
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
KeyRefinement Restraint Deviation
s_zero_chiral_vol94
s_non_zero_chiral_vol1
s_angle_d0.822
s_anti_bump_dis_restr0.128
s_similar_adp_cmpnt0.022
s_bond_d0.006
s_from_restr_planes0.005
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms194
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms36

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
SHELXphasing
SHELXrefinement
PDB_EXTRACTdata extraction