3B3X

Crystal structure of class A beta-lactamase of Bacillus licheniformis BS3 with aminocitrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W7FPDB ENTRY 1W7F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop7.22935micro-l of a protein solution (at a concentration of 38mg/ml in 50mM NaCl, 10mM Tris buffer, pH 7.2), 4micro-l of 8% PEG 6000 in 100mM sodium aminocitrate buffer (pH 3.4) plus 1micro-l of 0.1M urea additive, equilibrated against 1ml of a 20% PEG 6000, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.665α = 90
b = 104.71β = 93.96
c = 63.884γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2005-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.563.75882.30.0830.0837.61.917440
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.6475.50.3710.3711.91.72310

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 1W7F2.536.471739388781.880.2230.220.288RANDOM22.959
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]
0.050.06-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.223
r_dihedral_angle_3_deg19.146
r_dihedral_angle_4_deg18.802
r_dihedral_angle_1_deg7.666
r_scangle_it2.964
r_scbond_it1.857
r_angle_refined_deg1.834
r_mcangle_it1.354
r_mcbond_it0.778
r_symmetry_hbond_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.223
r_dihedral_angle_3_deg19.146
r_dihedral_angle_4_deg18.802
r_dihedral_angle_1_deg7.666
r_scangle_it2.964
r_scbond_it1.857
r_angle_refined_deg1.834
r_mcangle_it1.354
r_mcbond_it0.778
r_symmetry_hbond_refined0.316
r_nbtor_refined0.315
r_nbd_refined0.286
r_symmetry_vdw_refined0.268
r_xyhbond_nbd_refined0.226
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3988
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms26

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction