3MM3

Dye-decolorizing peroxidase (DyP) D171N in complex with cyanide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D3Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6278PEG 8000, pH 6.0, vapor diffusion, hanging drop, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.0740.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.954α = 90
b = 97.15β = 104.04
c = 46.46γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702009-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.000Photon FactoryAR-NE3A

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
11.450990.0515.83.775208
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)
11.41.42980.2613.63682

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 REPLACEMENTTHROUGHOUT2D3Q1.448.5675184378598.870.1820.1810.189RANDOM11.256
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]
0.410.05-0.590.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.14
r_dihedral_angle_4_deg22.669
r_dihedral_angle_3_deg10.44
r_dihedral_angle_1_deg5.769
r_scangle_it2.511
r_scbond_it1.612
r_angle_refined_deg1.203
r_mcangle_it1.104
r_mcbond_it0.587
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.14
r_dihedral_angle_4_deg22.669
r_dihedral_angle_3_deg10.44
r_dihedral_angle_1_deg5.769
r_scangle_it2.511
r_scbond_it1.612
r_angle_refined_deg1.203
r_mcangle_it1.104
r_mcbond_it0.587
r_chiral_restr0.084
r_bond_refined_d0.008
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3338
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms45

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction