1W05

Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Alanine-Fe Complex


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 (PH8.5), pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.2645

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.77α = 90
b = 101.77β = 90
c = 115.68γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1997-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200BH

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
12.4630970.1193104834
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)
12.462.541000.5813.1

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 1BK02.4687.7123745101296.50.1620.160.214RANDOM24.1
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]
-1.04-0.52-1.041.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.742
r_scangle_it4.786
r_scbond_it3.187
r_angle_refined_deg2.194
r_mcangle_it1.749
r_angle_other_deg1.121
r_mcbond_it1.026
r_symmetry_vdw_other0.333
r_symmetry_hbond_refined0.269
r_symmetry_vdw_refined0.268
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.742
r_scangle_it4.786
r_scbond_it3.187
r_angle_refined_deg2.194
r_mcangle_it1.749
r_angle_other_deg1.121
r_mcbond_it1.026
r_symmetry_vdw_other0.333
r_symmetry_hbond_refined0.269
r_symmetry_vdw_refined0.268
r_nbd_other0.256
r_nbd_refined0.221
r_xyhbond_nbd_refined0.195
r_chiral_restr0.156
r_nbtor_other0.097
r_bond_refined_d0.03
r_gen_planes_other0.021
r_gen_planes_refined0.015
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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 Atoms2633
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
Agrovatadata scaling
SCALAdata scaling