2OPW

Crystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherModel built from sulfur SAD data

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72937% PEG3350, 200mM Calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0759.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.97α = 90
b = 91.97β = 90
c = 81.61γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.95520SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.940.06990.12107318323183222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9292.52.246

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTModel built from sulfur SAD data1.940.062989229892158599.060.221080.221080.21910.25793RANDOM17.811
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]
0.950.470.95-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.112
r_dihedral_angle_4_deg21.689
r_dihedral_angle_3_deg15.772
r_scangle_it8.866
r_scbond_it6.755
r_dihedral_angle_1_deg6.637
r_mcangle_it4.214
r_mcbond_it3.261
r_angle_refined_deg1.569
r_angle_other_deg0.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.112
r_dihedral_angle_4_deg21.689
r_dihedral_angle_3_deg15.772
r_scangle_it8.866
r_scbond_it6.755
r_dihedral_angle_1_deg6.637
r_mcangle_it4.214
r_mcbond_it3.261
r_angle_refined_deg1.569
r_angle_other_deg0.941
r_mcbond_other0.92
r_symmetry_vdw_refined0.573
r_symmetry_vdw_other0.263
r_nbd_refined0.205
r_nbd_other0.201
r_nbtor_refined0.191
r_xyhbond_nbd_refined0.175
r_symmetry_hbond_refined0.096
r_nbtor_other0.094
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2214
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XDSdata scaling
PHASERphasing