5K1L

Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27715 % PEG 4000 150 mM Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.3146.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.79α = 90
b = 68.3β = 90
c = 68.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9282DiamondI04-1

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
11.0845.4199.80.0490.99916.76.9122447
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)
11.081.1199.81.441.25.5

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 REPLACEMENTTHROUGHOUT3IXF1.0845.41116192617199.80.15210.15070.1772RANDOM17.915
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]
0.52-0.880.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.61
r_sphericity_free28.612
r_dihedral_angle_4_deg25.307
r_dihedral_angle_3_deg12.64
r_sphericity_bonded11.425
r_rigid_bond_restr6.305
r_dihedral_angle_1_deg5.445
r_mcangle_it2.868
r_mcbond_it2.459
r_mcbond_other2.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.61
r_sphericity_free28.612
r_dihedral_angle_4_deg25.307
r_dihedral_angle_3_deg12.64
r_sphericity_bonded11.425
r_rigid_bond_restr6.305
r_dihedral_angle_1_deg5.445
r_mcangle_it2.868
r_mcbond_it2.459
r_mcbond_other2.459
r_angle_other_deg2.064
r_angle_refined_deg1.751
r_chiral_restr0.145
r_bond_refined_d0.019
r_gen_planes_other0.018
r_gen_planes_refined0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2162
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms119

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing