2VAU

Isopenicillin N synthase with substrate analogue 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
1.9937.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.697α = 90
b = 71.161β = 90
c = 100.912γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2005-04-17MSINGLE 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
11.834.398.40.12193192613.47
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)
11.791.89890.277.28.5

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 1BK01.830.4130604124599.80.1520.1510.19RANDOM5.5
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]
0.040.03-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.828
r_dihedral_angle_3_deg12.53
r_dihedral_angle_4_deg9.133
r_dihedral_angle_1_deg6.422
r_scangle_it3.861
r_scbond_it2.785
r_angle_other_deg2.235
r_angle_refined_deg1.722
r_mcangle_it1.446
r_mcbond_it1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.828
r_dihedral_angle_3_deg12.53
r_dihedral_angle_4_deg9.133
r_dihedral_angle_1_deg6.422
r_scangle_it3.861
r_scbond_it2.785
r_angle_other_deg2.235
r_angle_refined_deg1.722
r_mcangle_it1.446
r_mcbond_it1.24
r_symmetry_vdw_other0.288
r_nbd_other0.221
r_nbd_refined0.218
r_nbtor_refined0.185
r_symmetry_hbond_refined0.184
r_symmetry_vdw_refined0.169
r_xyhbond_nbd_refined0.159
r_chiral_restr0.114
r_nbtor_other0.086
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_gen_planes_other0.007
r_bond_other_d0.002
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 Atoms345
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing