8YYP | pdb_00008yyp

Crystal structure of PtmB in complex with cyclo-(L-Trp-L-Trp) and Adenine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1M Bis-Tris pH 5.5 0.2M Ammonium acetate 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.6253.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.453α = 90
b = 84.453β = 90
c = 133.377γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9785SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.625.0199.870.15490.99817.2913.728724
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6931000.85113.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.625.0128724143999.870.171020.20640.20710.25690.2556RANDOM40.63
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]
0.730.73-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.552
r_dihedral_angle_4_deg18.462
r_dihedral_angle_3_deg17.057
r_long_range_B_other8.645
r_long_range_B_refined8.636
r_dihedral_angle_1_deg7.35
r_scangle_other6.04
r_mcangle_it5.954
r_mcangle_other5.953
r_scbond_it3.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.552
r_dihedral_angle_4_deg18.462
r_dihedral_angle_3_deg17.057
r_long_range_B_other8.645
r_long_range_B_refined8.636
r_dihedral_angle_1_deg7.35
r_scangle_other6.04
r_mcangle_it5.954
r_mcangle_other5.953
r_scbond_it3.958
r_scbond_other3.957
r_mcbond_it3.882
r_mcbond_other3.882
r_angle_refined_deg1.637
r_angle_other_deg1.288
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5916
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms134

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction