4P85

Crystal structure of Est-Y29, a novel penicillin-binding protein/beta-lactamase homolog from a metagenomic library


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2871 M sodium citrate and 100 mM sodium acetate, pH 4.6
Crystal Properties
Matthews coefficientSolvent content
3.2762.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.081α = 90
b = 122.081β = 90
c = 155.288γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4A1.00000PAL/PLS4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9950100307.577368

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 DIFFRACTIONTHROUGHOUT229.0967804357793.390.19480.193090.22735RANDOM18.346
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
r_dihedral_angle_2_deg34.165
r_dihedral_angle_4_deg19.265
r_dihedral_angle_3_deg13.429
r_dihedral_angle_1_deg5.484
r_scangle_it2.664
r_scbond_it1.728
r_angle_refined_deg1.254
r_mcangle_it0.955
r_mcbond_it0.522
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.165
r_dihedral_angle_4_deg19.265
r_dihedral_angle_3_deg13.429
r_dihedral_angle_1_deg5.484
r_scangle_it2.664
r_scbond_it1.728
r_angle_refined_deg1.254
r_mcangle_it0.955
r_mcbond_it0.522
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.006
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6010
Nucleic Acid Atoms
Solvent Atoms754
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement