3IIQ | pdb_00003iiq

Crystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T7DPDB ENTRY 1T7D CHAIN A WITH LIGANDS REMOVED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2M NH4 FORMATE, 25% PEG 2000, 0.1M NA CACODYLATE PH 6.5, AND 5% TERTIARY-AMYL ALCOHOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
2.8456.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.007α = 90
b = 70.007β = 90
c = 259.894γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2007-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.2ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
1267.495.20.0680.06910.47.140272214
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1495.10.430.0525.14.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1T7D CHAIN A WITH LIGANDS REMOVED267.438237203595.10.210.2070.240.250.28RANDOM40.59
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]
1.171.17-2.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.365
r_dihedral_angle_3_deg15.882
r_dihedral_angle_4_deg14.229
r_dihedral_angle_1_deg9.383
r_scangle_it4.368
r_scbond_it3.301
r_angle_refined_deg2.348
r_mcangle_it2.334
r_mcbond_it1.824
r_nbtor_refined0.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.365
r_dihedral_angle_3_deg15.882
r_dihedral_angle_4_deg14.229
r_dihedral_angle_1_deg9.383
r_scangle_it4.368
r_scbond_it3.301
r_angle_refined_deg2.348
r_mcangle_it2.334
r_mcbond_it1.824
r_nbtor_refined0.325
r_chiral_restr0.321
r_symmetry_vdw_refined0.262
r_nbd_refined0.247
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.194
r_bond_refined_d0.03
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3573
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms114

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling