3SD9

Crystal structure of serratia fonticola SFH-I: Source of the nucleophile in the catalytic mechanism of mono-zinc metallo-beta-lactamases


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X8G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729325% PEG 3350, 0.1M AMMONIUM NITRATE, 3% ISOPROPANOL, PH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9637.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.965α = 90
b = 86.412β = 90.07
c = 72.193γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2008-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9529DiamondI04

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
11.8372.2940.0712.82.53535433217
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)
11.831.994.30.4522.33348

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 REPLACEMENTTHROUGHOUT1X8G1.8372.19315291663930.184840.183320.21311RANDOM11.27
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]
-1.44-0.760.560.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.775
r_dihedral_angle_4_deg22.005
r_dihedral_angle_3_deg13.707
r_dihedral_angle_1_deg6.014
r_sphericity_free4.18
r_scangle_it2.811
r_scbond_it1.892
r_sphericity_bonded1.778
r_angle_refined_deg1.334
r_mcangle_it1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.775
r_dihedral_angle_4_deg22.005
r_dihedral_angle_3_deg13.707
r_dihedral_angle_1_deg6.014
r_sphericity_free4.18
r_scangle_it2.811
r_scbond_it1.892
r_sphericity_bonded1.778
r_angle_refined_deg1.334
r_mcangle_it1.14
r_rigid_bond_restr1.115
r_mcbond_it0.735
r_chiral_restr0.091
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3637
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms2

Software

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