3ZOI

ISOPENICILLIN N SYNTHASE WITH AC-O-METHYL-D-THREONINE


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 TRIPEPTIDE, 25MG/ML IPNS
Crystal Properties
Matthews coefficientSolvent content
2.2244.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.48α = 90
b = 70.79β = 90
c = 100.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1998-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.812198.20.0614.33.23090421.2
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)
11.811.9192.10.342.92.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BK01.8211.9628870118198.080.162110.160410.20181RANDOM20.05
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]
-0.381.88-1.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_3_deg12.862
r_dihedral_angle_4_deg7.298
r_dihedral_angle_1_deg6.456
r_angle_refined_deg1.818
r_scbond_it1.662
r_mcangle_it1.315
r_angle_other_deg0.924
r_mcbond_it0.901
r_mcbond_other0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_3_deg12.862
r_dihedral_angle_4_deg7.298
r_dihedral_angle_1_deg6.456
r_angle_refined_deg1.818
r_scbond_it1.662
r_mcangle_it1.315
r_angle_other_deg0.924
r_mcbond_it0.901
r_mcbond_other0.9
r_chiral_restr0.243
r_bond_refined_d0.02
r_gen_planes_refined0.011
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_mcangle_other
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 Atoms2640
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling