5A1F

Crystal structure of the catalytic domain of PLU1 in complex with N-oxalylglycine.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GIOPDB ENTRY 4GIO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.1M HEPES PH 8.0, 0.8M POTASSIUM PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC
Crystal Properties
Matthews coefficientSolvent content
4.1870.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.855α = 90
b = 141.855β = 90
c = 152.129γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287CCDADSC QUANTUM 3152015-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
12.119.771000.0919.1411.5529702.6
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)
12.12.181000.092.4211.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4GIO2.150.0150341262999.770.20060.199310.22501RANDOM47.6
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]
0.410.20.41-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.102
r_dihedral_angle_4_deg17.544
r_dihedral_angle_3_deg15.113
r_dihedral_angle_1_deg6.391
r_mcangle_it4.623
r_scbond_it3.638
r_mcbond_it3.07
r_mcbond_other3.064
r_angle_refined_deg1.503
r_angle_other_deg0.985
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.102
r_dihedral_angle_4_deg17.544
r_dihedral_angle_3_deg15.113
r_dihedral_angle_1_deg6.391
r_mcangle_it4.623
r_scbond_it3.638
r_mcbond_it3.07
r_mcbond_other3.064
r_angle_refined_deg1.503
r_angle_other_deg0.985
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms3603
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
CCP4Iphasing