7M1K | pdb_00007m1k

Crystal structure of dehaloperoxidase B in complex with 2,6-difluorophenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IXF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277ammonium sulfate, sodium cacodylate, MPEG 2000
Crystal Properties
Matthews coefficientSolvent content
2.1843.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.145α = 90
b = 66.697β = 90
c = 68.028γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.7937.12294.220.99418.93.524292
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7951.8420.776

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3ixf1.79537.12224292121794.2240.1740.17130.180.22330.2320.37
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]
1.3110.085-1.396
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.33
r_dihedral_angle_4_deg19.104
r_dihedral_angle_3_deg18.251
r_dihedral_angle_1_deg5.968
r_lrange_it4.652
r_lrange_other4.612
r_scangle_it2.911
r_scangle_other2.911
r_scbond_it1.942
r_scbond_other1.937
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2137
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms144

Software

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