3MKE

SHV-1 beta-lactamase complex with LP06


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
1.9938.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.554α = 90
b = 56.484β = 90
c = 82.067γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.91840APS19-ID

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
11.755024.10.1114.223654111.338
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)
1.751.8199.40.4742.784.12334

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 1VM11.7533.922365422409120698.840.154680.153210.18107RANDOM11.271
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_deg35.323
r_dihedral_angle_4_deg19.978
r_dihedral_angle_3_deg12.652
r_dihedral_angle_1_deg5.901
r_scangle_it3.158
r_scbond_it1.988
r_angle_refined_deg1.564
r_mcangle_it1.037
r_mcbond_it0.664
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.323
r_dihedral_angle_4_deg19.978
r_dihedral_angle_3_deg12.652
r_dihedral_angle_1_deg5.901
r_scangle_it3.158
r_scbond_it1.988
r_angle_refined_deg1.564
r_mcangle_it1.037
r_mcbond_it0.664
r_nbtor_refined0.304
r_chiral_restr0.234
r_symmetry_vdw_refined0.202
r_nbd_refined0.2
r_symmetry_hbond_refined0.149
r_xyhbond_nbd_refined0.128
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms219
Heterogen Atoms98

Software

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