3MKF

SHV-1 beta-lactamase complex with GB0301


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729320-30% PEG 6000, 0.1M HEPES, 0.56Mm Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
1.9737.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.215α = 90
b = 56.139β = 90
c = 82.59γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.08100NSLSX29A

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
11.3350230.0344.449901112.191
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)
1.331.3873.50.2293.892.93850

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1VM11.3324.034990147303253393.550.179440.17890.18954RANDOM12.14
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_deg37.066
r_dihedral_angle_4_deg17.321
r_dihedral_angle_3_deg11.98
r_dihedral_angle_1_deg5.713
r_scangle_it2.31
r_scbond_it1.451
r_angle_refined_deg1.168
r_mcangle_it0.914
r_mcbond_it0.57
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.066
r_dihedral_angle_4_deg17.321
r_dihedral_angle_3_deg11.98
r_dihedral_angle_1_deg5.713
r_scangle_it2.31
r_scbond_it1.451
r_angle_refined_deg1.168
r_mcangle_it0.914
r_mcbond_it0.57
r_nbtor_refined0.303
r_nbd_refined0.197
r_symmetry_vdw_refined0.192
r_xyhbond_nbd_refined0.112
r_symmetry_hbond_refined0.095
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2024
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms70

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling