3S4X

Crystal structure of the Asn152Gly mutant of P99 beta-lactamase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.15 M ammonium sulfate, 30% polyethylene glycol (PEG) 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1843.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.956α = 90
b = 85.481β = 90
c = 51.681γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.1APS21-ID-D

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
11.955098.30.10410.925774-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0298.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1XX21.953524475129797.70.17850.175680.23359RANDOM29.865
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]
2.17-0.26-1.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.642
r_dihedral_angle_4_deg18.579
r_dihedral_angle_3_deg14.651
r_dihedral_angle_1_deg5.836
r_scangle_it5.121
r_scbond_it3.364
r_mcangle_it1.929
r_angle_refined_deg1.324
r_mcbond_it1.158
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.642
r_dihedral_angle_4_deg18.579
r_dihedral_angle_3_deg14.651
r_dihedral_angle_1_deg5.836
r_scangle_it5.121
r_scbond_it3.364
r_mcangle_it1.929
r_angle_refined_deg1.324
r_mcbond_it1.158
r_chiral_restr0.117
r_bond_refined_d0.023
r_gen_planes_refined0.011
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 Atoms2802
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms35

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling