2V2E

Structure of isoniazid (INH) bound to cytochrome c peroxidase mutant N184R Y36A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V23PDB ENTRY 2V23

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS6MICRODIALYSIS INTO 50MM POTASSIUM PHOSPHATE, PH 6.0 CONTAINING 30% V/V MPD. ISONIAZID WAS DISSOLVED INTO THE MOTHER LIQUOR (300MM) AND SOAKED INTO THE CRYSTAL.
Crystal Properties
Matthews coefficientSolvent content
3.0659.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.147α = 90
b = 75.13β = 90
c = 106.864γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEXENOCS MULTI-LAYERMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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
11.6830.2881.90.0327.43.338990
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)
11.681.7720.30.135.81.2

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 2V231.6830.2836963198382.20.1660.1650.187RANDOM13.15
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]
0.1-0.03-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.871
r_dihedral_angle_4_deg24.182
r_dihedral_angle_3_deg12.348
r_dihedral_angle_1_deg5.317
r_scangle_it2.376
r_scbond_it1.607
r_angle_refined_deg1.131
r_mcangle_it1.033
r_mcbond_it0.665
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.871
r_dihedral_angle_4_deg24.182
r_dihedral_angle_3_deg12.348
r_dihedral_angle_1_deg5.317
r_scangle_it2.376
r_scbond_it1.607
r_angle_refined_deg1.131
r_mcangle_it1.033
r_mcbond_it0.665
r_nbtor_refined0.304
r_nbd_refined0.194
r_symmetry_vdw_refined0.187
r_symmetry_hbond_refined0.118
r_xyhbond_nbd_refined0.102
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 Atoms2340
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing