8JK3

Crystal Structure of Bel-1 Extended Spectrum Beta-lactamase in Hexagonal Form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EOE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.2M Magnesium chloride hexahydrate, 0.1M HEPES sodium pH 7.5, 30% v/v 2-Propanol
Crystal Properties
Matthews coefficientSolvent content
2.6353.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.192α = 90
b = 121.192β = 90
c = 72.128γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HEX ray optics2022-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.529.12699.90.9918.47.696340
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.58.220.418

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.529.12696119497599.7510.1530.150.208820.523
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]
-0.048-0.024-0.0480.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.773
r_dihedral_angle_3_deg13.635
r_dihedral_angle_2_deg9.008
r_dihedral_angle_1_deg6.103
r_rigid_bond_restr5.93
r_lrange_it4.403
r_lrange_other4.398
r_scangle_it3.476
r_scangle_other3.476
r_scbond_it2.702
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.773
r_dihedral_angle_3_deg13.635
r_dihedral_angle_2_deg9.008
r_dihedral_angle_1_deg6.103
r_rigid_bond_restr5.93
r_lrange_it4.403
r_lrange_other4.398
r_scangle_it3.476
r_scangle_other3.476
r_scbond_it2.702
r_scbond_other2.702
r_mcangle_other2.532
r_mcangle_it2.526
r_mcbond_it2.018
r_angle_refined_deg2.009
r_mcbond_other2.003
r_angle_other_deg0.675
r_metal_ion_refined0.454
r_symmetry_xyhbond_nbd_refined0.275
r_symmetry_nbd_refined0.255
r_nbd_refined0.239
r_xyhbond_nbd_refined0.227
r_nbd_other0.209
r_symmetry_nbd_other0.184
r_nbtor_refined0.183
r_chiral_restr0.104
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.053
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4063
Nucleic Acid Atoms
Solvent Atoms608
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing