2V1Z

Structure of a TEM-1 beta-lactamase insertant allosterically regulated by kanamycin and anions.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BTLPDB ENTRY 1BTL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2RESERVOIR: BIS-TRIS 0.1M PH6.2, PEG6000 25%(W/V), NACL 0.3M, NAN3 0.02%(W/V). HANGING DROP: 1UL PROTEIN AND 1 UL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
238.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.113α = 90
b = 70.609β = 90
c = 78.313γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHTWO MIRRORS ARE USED FOR VERTICAL FOCUSSING.2005-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
11.64096.70.0423.93.534091
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)
11.61.6593.20.228.23.1

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 1BTL1.652.4132339171096.80.1710.1690.206RANDOM15.04
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_deg34.593
r_dihedral_angle_4_deg15.851
r_dihedral_angle_3_deg12.323
r_dihedral_angle_1_deg5.394
r_scangle_it3.973
r_scbond_it2.749
r_angle_refined_deg1.672
r_mcangle_it1.599
r_mcbond_it1.437
r_angle_other_deg1.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.593
r_dihedral_angle_4_deg15.851
r_dihedral_angle_3_deg12.323
r_dihedral_angle_1_deg5.394
r_scangle_it3.973
r_scbond_it2.749
r_angle_refined_deg1.672
r_mcangle_it1.599
r_mcbond_it1.437
r_angle_other_deg1.065
r_symmetry_vdw_refined0.225
r_nbd_refined0.22
r_symmetry_vdw_other0.209
r_nbd_other0.203
r_nbtor_refined0.174
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.142
r_chiral_restr0.106
r_nbtor_other0.088
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms2095
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing