2X66

The binary complex of PrnB (the second enzyme in pyrrolnitrin biosynthesis pathway) 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
2.957.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.364α = 90
b = 79.305β = 102.9
c = 91.752γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDOSMIC MIRRORS2008-04-08MSINGLE 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
12.092698.20.1132.427803226.2
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)
12.092.14940.422.22

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 2V7J2.0925.5826371142998.230.178090.175740.22194RANDOM13.7
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]
0.1-0.730.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.475
r_dihedral_angle_4_deg18.525
r_dihedral_angle_3_deg13.48
r_dihedral_angle_1_deg5.232
r_scangle_it3.542
r_scbond_it2.107
r_angle_refined_deg1.32
r_mcangle_it1.215
r_mcbond_it0.662
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.475
r_dihedral_angle_4_deg18.525
r_dihedral_angle_3_deg13.48
r_dihedral_angle_1_deg5.232
r_scangle_it3.542
r_scbond_it2.107
r_angle_refined_deg1.32
r_mcangle_it1.215
r_mcbond_it0.662
r_chiral_restr0.089
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 Atoms2690
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms50

Software

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