6VDT

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-nitrophenol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.2 M Ammonium Sulphate MPEG 2000, 29-33%
Crystal Properties
Matthews coefficientSolvent content
2.1943.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.7α = 90
b = 67.66β = 90
c = 67.73γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2019-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-BM

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
11.7747.9995.570.99920.94.225924
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)
11.771.820.6

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3IXF1.97837.0971808793293.1260.170.1670.222926.366
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]
9.816-3.008-6.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.614
r_dihedral_angle_4_deg22.29
r_dihedral_angle_3_deg19.699
r_lrange_it7.378
r_lrange_other7.35
r_dihedral_angle_1_deg6.101
r_scangle_it2.434
r_scangle_other2.427
r_angle_refined_deg2.384
r_mcangle_it2.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.614
r_dihedral_angle_4_deg22.29
r_dihedral_angle_3_deg19.699
r_lrange_it7.378
r_lrange_other7.35
r_dihedral_angle_1_deg6.101
r_scangle_it2.434
r_scangle_other2.427
r_angle_refined_deg2.384
r_mcangle_it2.263
r_mcangle_other2.263
r_scbond_it1.608
r_scbond_other1.591
r_angle_other_deg1.466
r_mcbond_it1.369
r_mcbond_other1.368
r_nbd_refined0.275
r_xyhbond_nbd_refined0.218
r_nbd_other0.215
r_symmetry_nbd_other0.206
r_symmetry_xyhbond_nbd_other0.192
r_nbtor_refined0.183
r_symmetry_xyhbond_nbd_refined0.16
r_symmetry_nbd_refined0.153
r_chiral_restr0.14
r_symmetry_nbtor_other0.085
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_gen_planes_other0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2134
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing