2CKJ | pdb_00002ckj

Human milk xanthine oxidoreductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FO4PDB ENTRY 1FO4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1626% (W/V) PEG 4K, 0.1M SODIUM ACETATE, PH 6, 0.25M AMMONIUM ACETATE, 10MM DTT, 10% (W/V) GLUCOSE
Crystal Properties
Matthews coefficientSolvent content
2.753.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 197.734α = 90
b = 197.734β = 90
c = 285.538γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
13.53098.20.123.64.4750881.5
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)
13.53.6295.30.471.53.5

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-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FO43.5930.7670696374598.20.1820.1780.258RANDOM22.75
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.738
r_dihedral_angle_3_deg25.79
r_dihedral_angle_4_deg22.106
r_dihedral_angle_1_deg15.08
r_scangle_it3.993
r_angle_refined_deg3.461
r_scbond_it2.564
r_mcangle_it1.759
r_mcbond_it1.193
r_symmetry_vdw_refined0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.738
r_dihedral_angle_3_deg25.79
r_dihedral_angle_4_deg22.106
r_dihedral_angle_1_deg15.08
r_scangle_it3.993
r_angle_refined_deg3.461
r_scbond_it2.564
r_mcangle_it1.759
r_mcbond_it1.193
r_symmetry_vdw_refined0.36
r_nbtor_refined0.354
r_nbd_refined0.317
r_chiral_restr0.221
r_xyhbond_nbd_refined0.218
r_symmetry_hbond_refined0.182
r_bond_refined_d0.045
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms39530
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms277

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing