1W06

Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Alanine-Fe NO 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 = 47.13α = 90
b = 71.45β = 90
c = 101.88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1997-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.652292.30.1152.838692
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)
11.651.69850.4092.9

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 1BK01.6558.7237099159391.70.1710.170.204RANDOM10.42
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]
0.090.7-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.147
r_scbond_it2.687
r_angle_other_deg1.741
r_mcangle_it1.649
r_mcbond_it0.999
r_dihedral_angle_3_deg0.869
r_xyhbond_nbd_other0.367
r_symmetry_vdw_refined0.284
r_nbd_refined0.229
r_symmetry_vdw_other0.219
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.147
r_scbond_it2.687
r_angle_other_deg1.741
r_mcangle_it1.649
r_mcbond_it0.999
r_dihedral_angle_3_deg0.869
r_xyhbond_nbd_other0.367
r_symmetry_vdw_refined0.284
r_nbd_refined0.229
r_symmetry_vdw_other0.219
r_xyhbond_nbd_refined0.217
r_symmetry_hbond_refined0.199
r_nbd_other0.195
r_chiral_restr0.116
r_nbtor_other0.078
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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 Atoms2641
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
Agrovatadata scaling
SCALAdata scaling