7QOR

Structure of beta-lactamase TEM-171


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JYI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277PEG-4000, 0.2 M calcium acetate, 0.1 M Tris-HCl, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.7955.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.19α = 90
b = 88.19β = 90
c = 499.323γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.976300PETRA III, EMBL c/o DESYP14 (MX2)

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
11.99986.8598.60.9918.513.2132474
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)
11.9992.050.787

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-VALUE3JYI1.99915132051652697.8340.1910.18990.210658.018
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]
1.3631.363-2.727
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.463
r_dihedral_angle_4_deg15.345
r_dihedral_angle_3_deg13.932
r_lrange_it7.314
r_lrange_other7.257
r_dihedral_angle_1_deg6.406
r_scangle_it2.418
r_scangle_other2.418
r_mcangle_it1.901
r_mcangle_other1.901
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.463
r_dihedral_angle_4_deg15.345
r_dihedral_angle_3_deg13.932
r_lrange_it7.314
r_lrange_other7.257
r_dihedral_angle_1_deg6.406
r_scangle_it2.418
r_scangle_other2.418
r_mcangle_it1.901
r_mcangle_other1.901
r_angle_refined_deg1.558
r_scbond_it1.448
r_scbond_other1.448
r_angle_other_deg1.356
r_mcbond_it1.17
r_mcbond_other1.17
r_nbd_other0.229
r_symmetry_xyhbond_nbd_refined0.219
r_nbd_refined0.195
r_symmetry_nbd_other0.185
r_xyhbond_nbd_refined0.183
r_nbtor_refined0.153
r_symmetry_nbd_refined0.094
r_symmetry_nbtor_other0.083
r_chiral_restr0.077
r_symmetry_xyhbond_nbd_other0.044
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12168
Nucleic Acid Atoms
Solvent Atoms875
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing