2X67

The ternary complex of PrnB (the second enzyme in pyrrolnitrin biosynthesis pathway), tryptophan and cyanide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V7JPDB ENTRY 2V7J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.40.1M BIS-TRIS BUFFER PH 6.4, 10% PEG3350, 0.2M MGSO4
Crystal Properties
Matthews coefficientSolvent content
2.957.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.392α = 90
b = 79.441β = 103.17
c = 92.058γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDOSMIC MIRRORS2008-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.163099.80.115.63.524411227.2
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)
12.162.299.50.463.43.4

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 2V7J2.1629.8424411133099.790.167880.165560.21073RANDOM15.024
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]
0.10.56-0.730.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.548
r_dihedral_angle_4_deg22.61
r_dihedral_angle_3_deg14.657
r_dihedral_angle_1_deg5.057
r_scangle_it3.466
r_scbond_it2.122
r_angle_refined_deg1.371
r_mcangle_it1.167
r_mcbond_it0.638
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.548
r_dihedral_angle_4_deg22.61
r_dihedral_angle_3_deg14.657
r_dihedral_angle_1_deg5.057
r_scangle_it3.466
r_scbond_it2.122
r_angle_refined_deg1.371
r_mcangle_it1.167
r_mcbond_it0.638
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms2737
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling