5W90

FEZ-1 metallo-beta-lactamase from Legionella gormanii modelled with unknown ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JT1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293.1518% PEG MME5000, 0.2M ammonium sulfate, 0.1M HEPES 7.0, 0.010MM Zn chloride, 0.0108MM D-CAPTOPRIL, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.2745.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.12α = 90
b = 76.775β = 110.21
c = 44.841γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2001-04-29MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A1.282760, 1.5418ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.7842.2692.40.0450.03814.33.245143
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.88610.0970.0768.41.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1JT11.7838.0820581233491.490.11610.11160.1549RANDOM16.538
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]
0.410.070.1-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.575
r_dihedral_angle_1_deg16.745
r_dihedral_angle_3_deg11.774
r_dihedral_angle_4_deg7.491
r_sphericity_bonded3.63
r_angle_refined_deg1.544
r_angle_other_deg1.014
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.575
r_dihedral_angle_1_deg16.745
r_dihedral_angle_3_deg11.774
r_dihedral_angle_4_deg7.491
r_sphericity_bonded3.63
r_angle_refined_deg1.544
r_angle_other_deg1.014
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2055
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
PDB_EXTRACTdata extraction