2VBD

Isopenicillin N synthase with substrate analogue L,L,L-ACOMP (unexposed)


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
2.0740.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.537α = 90
b = 71.314β = 90
c = 100.651γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2005-03-20MSINGLE 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
11.9918.1797.70.0919.56.62316017.57
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)
11.992.185.90.277.46.1

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 1BK0258.2222198909990.1690.1670.216RANDOM11.76
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]
-0.350.63-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.496
r_dihedral_angle_3_deg13.755
r_dihedral_angle_4_deg8.975
r_dihedral_angle_1_deg6.752
r_scangle_it4.281
r_scbond_it3.095
r_angle_refined_deg1.798
r_mcangle_it1.728
r_mcbond_it1.41
r_angle_other_deg1.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.496
r_dihedral_angle_3_deg13.755
r_dihedral_angle_4_deg8.975
r_dihedral_angle_1_deg6.752
r_scangle_it4.281
r_scbond_it3.095
r_angle_refined_deg1.798
r_mcangle_it1.728
r_mcbond_it1.41
r_angle_other_deg1.097
r_symmetry_vdw_other0.253
r_nbd_refined0.219
r_nbd_other0.195
r_nbtor_refined0.184
r_symmetry_vdw_refined0.157
r_xyhbond_nbd_refined0.15
r_chiral_restr0.116
r_symmetry_hbond_refined0.112
r_nbtor_other0.09
r_bond_refined_d0.024
r_bond_other_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.001
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 Atoms2645
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing