5LKV

Dehaloperoxidase B from Amphitrite ornata: imidazole complex


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.427712 mg/ml DHP B in 20 mM Na cacodylate (pH 6.4) was mixed with a reservoir solution comprising 14-20% (w/v) PEG 4000 and 150-250 mM ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.2645.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.359α = 90
b = 67.359β = 90
c = 67.522γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.0847.6995.80.0221333.61150287.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.081.1710.1130.8867.62.4

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 REPLACEMENTTHROUGHOUT3IXF1.0847.69109280567695.580.12310.12220.1406RANDOM11.182
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]
0.72-0.26-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.346
r_sphericity_free25.943
r_dihedral_angle_4_deg25.52
r_dihedral_angle_3_deg12.117
r_sphericity_bonded6.916
r_dihedral_angle_1_deg4.87
r_rigid_bond_restr2.518
r_angle_refined_deg1.633
r_mcangle_it1.143
r_angle_other_deg1.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.346
r_sphericity_free25.943
r_dihedral_angle_4_deg25.52
r_dihedral_angle_3_deg12.117
r_sphericity_bonded6.916
r_dihedral_angle_1_deg4.87
r_rigid_bond_restr2.518
r_angle_refined_deg1.633
r_mcangle_it1.143
r_angle_other_deg1.005
r_mcbond_it0.854
r_mcbond_other0.854
r_chiral_restr0.142
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.009
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2162
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms128

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing