5WCM

Crystal structure of the complex between class B3 beta-lactamase BJP-1 and 4-nitrobenzene-sulfonamide - new refinement


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LVZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29330-35% PEG 4000, 5MM ZNCL2, 0.5M SODIUM ACETATE, TRIS-HCL 0.1M, PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.1843.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.352α = 79.34
b = 44.908β = 90.59
c = 76.635γ = 61.68
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9340ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.25082.10.0440.0440.0490.02214.34.5124424-314.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.22320.2920.2920.3410.1750.9344.43.6

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 REPLACEMENTTHROUGHOUT3LVZ1.250117432608381.320.13340.1320.1598RANDOM18.358
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]
-0.140.04-0.030.06-0.030.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.841
r_sphericity_free18.732
r_dihedral_angle_4_deg11.637
r_sphericity_bonded11.372
r_dihedral_angle_3_deg11.314
r_dihedral_angle_1_deg5.798
r_rigid_bond_restr5.027
r_angle_refined_deg1.436
r_angle_other_deg1.064
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.841
r_sphericity_free18.732
r_dihedral_angle_4_deg11.637
r_sphericity_bonded11.372
r_dihedral_angle_3_deg11.314
r_dihedral_angle_1_deg5.798
r_rigid_bond_restr5.027
r_angle_refined_deg1.436
r_angle_other_deg1.064
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3974
Nucleic Acid Atoms
Solvent Atoms829
Heterogen Atoms37

Software

Software
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing