3HZL

Tyr258Phe mutant of NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: open form at 1.55A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OLOPDB entry 2OLO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.62984 mL of the Tyr258Phe mutant protein (at 10 mg/mL) was mixed with 4 mL 20-30% 2-methyl-2,4-pentanediol (MPD) in 100 mM MES buffer (pH 5.7) and equilibrated against a reservoir of the latter solution, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.4364.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.39α = 90
b = 90.53β = 118.36
c = 85.97γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 42008-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
11.555099.60.065276.28605822.5
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)
1.551.5997.40.40134.5

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 2OLO1.5538.8985842430899.50.2250.2250.244RANDOM26.6
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]
1.72-3.290.44-2.16
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_angle_deg5.4
c_improper_angle_d1.48
c_bond_d0.786
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_angle_deg5.4
c_improper_angle_d1.48
c_bond_d0.786
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3088
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms86

Software

Software
Software NamePurpose
ADSCdata collection
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing