1W03

Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Glycine-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 = 46.77α = 90
b = 71.2β = 90
c = 100.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1996-02-15MSINGLE 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
12.13098.20.1315.13.3620133
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)
12.12.1887.30.3783.62.9

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 1BK02.111.991923583699.60.1720.1710.197RANDOM16.79
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]
-0.31.3-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.914
r_scangle_it2.548
r_angle_refined_deg1.872
r_scbond_it1.812
r_angle_other_deg0.994
r_mcangle_it0.973
r_mcbond_it0.62
r_symmetry_vdw_other0.299
r_nbd_other0.265
r_nbd_refined0.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.914
r_scangle_it2.548
r_angle_refined_deg1.872
r_scbond_it1.812
r_angle_other_deg0.994
r_mcangle_it0.973
r_mcbond_it0.62
r_symmetry_vdw_other0.299
r_nbd_other0.265
r_nbd_refined0.208
r_symmetry_hbond_refined0.19
r_symmetry_vdw_refined0.189
r_xyhbond_nbd_refined0.16
r_chiral_restr0.106
r_nbtor_other0.089
r_bond_refined_d0.019
r_gen_planes_refined0.019
r_bond_other_d0.015
r_gen_planes_other0.014
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 Atoms2640
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling