2JB4

Isopenicillin N synthase with a 2-thiabicycloheptan-6-one product analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BK0PDB ENTRY 1BK0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.51.0M LITHIUM SULPHATE, 76MM TRIS/HCL, PH 8.5, 2.0MM FERROUS SULPHATE, 6.8 MM SUBSTRATE, 25MG/ML IPNS
Crystal Properties
Matthews coefficientSolvent content
2.2344.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.677α = 90
b = 71.273β = 90
c = 100.906γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDRH COATED TOROIDAL MIRRORS2003-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.330.996.30.0812.84.780123
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)
11.31.3778.40.452.12.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1BK01.357.7476025402396.20.1540.1530.176RANDOM7.95
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]
-0.160.45-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.266
r_dihedral_angle_4_deg14.314
r_dihedral_angle_3_deg11.041
r_dihedral_angle_1_deg6.168
r_scangle_it4.009
r_scbond_it2.848
r_angle_refined_deg1.82
r_angle_other_deg1.758
r_mcangle_it1.67
r_mcbond_it1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.266
r_dihedral_angle_4_deg14.314
r_dihedral_angle_3_deg11.041
r_dihedral_angle_1_deg6.168
r_scangle_it4.009
r_scbond_it2.848
r_angle_refined_deg1.82
r_angle_other_deg1.758
r_mcangle_it1.67
r_mcbond_it1.23
r_symmetry_vdw_other0.259
r_symmetry_vdw_refined0.229
r_nbd_refined0.221
r_nbd_other0.194
r_nbtor_refined0.193
r_xyhbond_nbd_refined0.193
r_symmetry_hbond_refined0.172
r_chiral_restr0.132
r_nbtor_other0.09
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2637
Nucleic Acid Atoms
Solvent Atoms403
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing