1GKF

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.2745.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.2α = 90
b = 131.7β = 105.7
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
11.42597.40.05219.82.415216312.7
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)
11.411.4382.50.1764.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4125147544458497.40.1480.168RANDOM14.4
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_it4.253
p_scbond_it3.395
p_mcangle_it1.987
p_mcbond_it1.509
p_chiral_restr0.131
p_planar_d0.038
p_angle_d0.031
p_plane_restr0.0255
p_bond_d0.018
p_angle_deg
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it4.253
p_scbond_it3.395
p_mcangle_it1.987
p_mcbond_it1.509
p_chiral_restr0.131
p_planar_d0.038
p_angle_d0.031
p_plane_restr0.0255
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 Atoms6075
Nucleic Acid Atoms
Solvent Atoms901
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing