2VCF

Structure of isoniazid (INH) bound to cytosolic soybean ascorbate peroxidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OAFPDB ENTRY 1OAF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.32.5M LISO4 PH 8.3
Crystal Properties
Matthews coefficientSolvent content
1.944.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.243α = 90
b = 82.243β = 90
c = 74.965γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
11.827.111000.0917.46.924461
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)
11.81.91000.384.77.09

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 1OAF1.826.012320512121000.1560.1540.188RANDOM16.94
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.499
r_dihedral_angle_4_deg19.714
r_dihedral_angle_3_deg11.973
r_dihedral_angle_1_deg5.314
r_scangle_it3.188
r_scbond_it2.063
r_mcangle_it1.387
r_angle_refined_deg1.234
r_mcbond_it0.827
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.499
r_dihedral_angle_4_deg19.714
r_dihedral_angle_3_deg11.973
r_dihedral_angle_1_deg5.314
r_scangle_it3.188
r_scbond_it2.063
r_mcangle_it1.387
r_angle_refined_deg1.234
r_mcbond_it0.827
r_nbtor_refined0.304
r_nbd_refined0.213
r_symmetry_vdw_refined0.211
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.134
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms1911
Nucleic Acid Atoms
Solvent Atoms383
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing