1GK9

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PNK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.2742.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.3α = 90
b = 131.6β = 105.9
c = 63.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.32095.50.07520.53.619022911.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.31820.2443.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PNK1.320181046565395.50.1480.169RANDOM15.5
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
p_scangle_it4.467
p_scbond_it3.388
p_mcangle_it1.982
p_mcbond_it1.536
p_chiral_restr0.128
p_planar_d0.04
p_angle_d0.031
p_plane_restr0.026
p_bond_d0.018
p_angle_deg
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it4.467
p_scbond_it3.388
p_mcangle_it1.982
p_mcbond_it1.536
p_chiral_restr0.128
p_planar_d0.04
p_angle_d0.031
p_plane_restr0.026
p_bond_d0.018
p_angle_deg
p_hb_or_metal_coord
p_singtor_nbd
p_multtor_nbd
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6086
Nucleic Acid Atoms
Solvent Atoms923
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing