1W04

Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Glycine-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 = 46.652α = 90
b = 70.752β = 90
c = 100.973γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1997-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.6SRSPX9.6

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
11.2816.192.60.07810.83.679915
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)
11.281.3585.30.3253.23.2

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 1BK01.2857.7476679317292.20.1630.1620.175RANDOM7.23
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]
-0.240.39-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.647
r_scangle_it3.329
r_scbond_it2.384
r_angle_refined_deg2.002
r_mcangle_it1.457
r_angle_other_deg1.026
r_mcbond_it0.923
r_nbd_refined0.337
r_symmetry_vdw_other0.293
r_metal_ion_refined0.266
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.647
r_scangle_it3.329
r_scbond_it2.384
r_angle_refined_deg2.002
r_mcangle_it1.457
r_angle_other_deg1.026
r_mcbond_it0.923
r_nbd_refined0.337
r_symmetry_vdw_other0.293
r_metal_ion_refined0.266
r_nbd_other0.247
r_xyhbond_nbd_refined0.156
r_chiral_restr0.155
r_symmetry_vdw_refined0.133
r_symmetry_hbond_refined0.106
r_nbtor_other0.088
r_bond_refined_d0.023
r_gen_planes_other0.017
r_gen_planes_refined0.016
r_bond_other_d0.003
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_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 Atoms2638
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling