4P6B

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2872.0 M sodium formate, 0.1 M sodium acetate trihydrate buffer (pH 4.6)
Crystal Properties
Matthews coefficientSolvent content
3.3463.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.541α = 90
b = 121.541β = 90
c = 155.173γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-03-08MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4A1.00000, 0.97888, 0.97917, 0.96395PAL/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
11.75099.5457.2122542

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 DIFFRACTIONTHROUGHOUT1.730115954612299.180.171310.170430.18793RANDOM19.102
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_deg34.753
r_dihedral_angle_4_deg20.746
r_dihedral_angle_3_deg12.609
r_dihedral_angle_1_deg5.608
r_scangle_it3.217
r_scbond_it1.986
r_angle_refined_deg1.253
r_mcangle_it1.208
r_mcbond_it0.64
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.753
r_dihedral_angle_4_deg20.746
r_dihedral_angle_3_deg12.609
r_dihedral_angle_1_deg5.608
r_scangle_it3.217
r_scbond_it1.986
r_angle_refined_deg1.253
r_mcangle_it1.208
r_mcbond_it0.64
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.007
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 Atoms5938
Nucleic Acid Atoms
Solvent Atoms898
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data scaling