3ZKU

Isopenicillin N synthase with substrate analogue AhCV


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, 2.6MG/ML SUBSTRATE, 25MG/ML IPNS
Crystal Properties
Matthews coefficientSolvent content
2.2646

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.48α = 90
b = 71.105β = 90
c = 101.045γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRROR2002-04-27MSINGLE 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
11.44299.40.0522.64.46642612.9
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)
11.41.4389.10.254.63.3

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 1BK01.441.2263701264699.310.162120.161250.1827RANDOM15.446
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]
0.060.4-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.263
r_dihedral_angle_4_deg14.683
r_dihedral_angle_3_deg12.034
r_dihedral_angle_1_deg6.489
r_angle_refined_deg2.039
r_angle_other_deg1.016
r_chiral_restr0.176
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.263
r_dihedral_angle_4_deg14.683
r_dihedral_angle_3_deg12.034
r_dihedral_angle_1_deg6.489
r_angle_refined_deg2.039
r_angle_other_deg1.016
r_chiral_restr0.176
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms2616
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling