4ICQ

Structural basis for substrate recognition and reaction mechanism of bacterial aminopeptidase peps


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.62M MAGNESIUM SULFATE, PH 4.6, MICROBATCH, TEMPERATURE 295K
Crystal Properties
Matthews coefficientSolvent content
3.0860.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.644α = 90
b = 126.644β = 90
c = 139.027γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER CCD PROTEUM 300MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6BPAL/PLS6B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2500.08346.0114.357898
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3199.60.4855.914.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2543.95152127601000.2020.1990.246RANDOM33.85
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]
-0.13-0.130.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.994
r_dihedral_angle_4_deg22.125
r_dihedral_angle_3_deg16.9
r_dihedral_angle_1_deg6.586
r_scangle_it5.248
r_scbond_it3.29
r_angle_refined_deg1.874
r_mcangle_it1.834
r_mcbond_it0.994
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.994
r_dihedral_angle_4_deg22.125
r_dihedral_angle_3_deg16.9
r_dihedral_angle_1_deg6.586
r_scangle_it5.248
r_scbond_it3.29
r_angle_refined_deg1.874
r_mcangle_it1.834
r_mcbond_it0.994
r_chiral_restr0.135
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6366
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms4

Software

Software
Software NamePurpose
ADSCdata collection
EPMRphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling