6VD6

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Mesoporphyrin 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
2.2144.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.138α = 90
b = 67.927β = 90
c = 67.867γ = 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
11.5637.394.480.99829.43.835281
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)
11.561.60.741

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-VALUE3IXF1.56337.337232195194.4830.1850.18360.216118.272
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]
0.891-0.444-0.447
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.34
r_dihedral_angle_4_deg26.497
r_dihedral_angle_3_deg16.391
r_dihedral_angle_other_2_deg11.652
r_dihedral_angle_1_deg5.962
r_lrange_it3.671
r_lrange_other3.638
r_scangle_it2.4
r_scangle_other2.371
r_angle_refined_deg2.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.34
r_dihedral_angle_4_deg26.497
r_dihedral_angle_3_deg16.391
r_dihedral_angle_other_2_deg11.652
r_dihedral_angle_1_deg5.962
r_lrange_it3.671
r_lrange_other3.638
r_scangle_it2.4
r_scangle_other2.371
r_angle_refined_deg2.001
r_angle_other_deg1.636
r_scbond_it1.584
r_scbond_other1.561
r_mcangle_it1.311
r_mcangle_other1.311
r_mcbond_it0.872
r_mcbond_other0.871
r_dihedral_angle_other_1_deg0.579
r_symmetry_nbd_refined0.297
r_nbd_other0.291
r_nbd_refined0.252
r_nbtor_refined0.192
r_symmetry_nbd_other0.184
r_xyhbond_nbd_refined0.158
r_symmetry_xyhbond_nbd_refined0.135
r_chiral_restr0.101
r_symmetry_nbtor_other0.085
r_symmetry_xyhbond_nbd_other0.058
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2159
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms124

Software

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