6MPZ | pdb_00006mpz

Crystal structure of a double glycine motif protease from AMS/PCAT transporter in complex with the leader peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52820.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.0 2M N-acetyl-D-glucosamine, 0.05 M Tris and BICINE pH 8.5, 20% v/v polyethylene glycol 500 monomethyl ether, 10% w/v polyethylene glycol 20000, and 8% v/v formamide
Crystal Properties
Matthews coefficientSolvent content
2.3948.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.888α = 90
b = 119.426β = 93.84
c = 76.522γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDRAYONIX MX-3002018-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.9876.499.89.35.147187
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.981.985

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 DIFFRACTIONTHROUGHOUT250.0143389230699.80.236060.234340.240.268290.27RANDOM37.026
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]
-2.160.47-4.376.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.875
r_dihedral_angle_4_deg21.581
r_dihedral_angle_3_deg17.864
r_dihedral_angle_1_deg7.612
r_long_range_B_refined7.414
r_long_range_B_other7.414
r_scangle_other5.392
r_mcangle_it4.392
r_mcangle_other4.391
r_scbond_it3.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.875
r_dihedral_angle_4_deg21.581
r_dihedral_angle_3_deg17.864
r_dihedral_angle_1_deg7.612
r_long_range_B_refined7.414
r_long_range_B_other7.414
r_scangle_other5.392
r_mcangle_it4.392
r_mcangle_other4.391
r_scbond_it3.54
r_scbond_other3.539
r_mcbond_it2.99
r_mcbond_other2.989
r_angle_refined_deg1.815
r_angle_other_deg1.033
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4843
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
AutoSolphasing
PHENIXmodel building