3QH8

Crystal structure of a beta-lactamase-like protein bound to AMP from brucella melitensis, long wavelength synchrotron data


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829015-18% PEG 3350, 200MM K/NA TARTRATE, 100MM BISTRISPROPANE PH 8.0, BRABA.11339.A.PW27637 AT 18MG/ML SUPPLEMENTED WITH 1MM AMPPNP AND 2MM MGCL2 AT 18MG/ML. CRYO: 21% PEG 3350, 15% EG, 165MM K/NA TARTRATE, 87MM BISTRISPROPANE PH 8.0, 1MM AMPPNP, 2MM MGCL2, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.2344.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.21α = 90
b = 75.53β = 90
c = 98.94γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.3476ALS5.0.2

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
11.62099.60.06925.0812.33651736362-320.91
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)
11.61.6495.90.395.86.136362

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUTPDB entry 3md71.618.883636236263186899.40.1450.1450.1430.166RANDOM10.64
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]
-0.2-0.20.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.757
r_dihedral_angle_4_deg16.3
r_dihedral_angle_3_deg10.998
r_dihedral_angle_1_deg6.181
r_scangle_it4.038
r_scbond_it2.549
r_mcangle_it1.657
r_angle_refined_deg1.652
r_angle_other_deg0.983
r_mcbond_it0.937
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.757
r_dihedral_angle_4_deg16.3
r_dihedral_angle_3_deg10.998
r_dihedral_angle_1_deg6.181
r_scangle_it4.038
r_scbond_it2.549
r_mcangle_it1.657
r_angle_refined_deg1.652
r_angle_other_deg0.983
r_mcbond_it0.937
r_mcbond_other0.286
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2118
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms40

Software

Software
Software NamePurpose
BOSdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling