4OTH

Crystal Structure of PRK1 Catalytic Domain in Complex with Ro-31-8220


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5100mM Tris pH 8.5, 150-225mM Ammonium acetate, 23-28% PEG 3350, Vapor diffusion
Crystal Properties
Matthews coefficientSolvent content
2.5251.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.319α = 90
b = 72.197β = 90
c = 94.903γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31ALS5.0.3

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
11.85092.80.04318.73.333917
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)
11.81.8384.10.2952.41511

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.836.2933191165390.930.20410.20090.266RANDOM29.687
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]
-0.510.060.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.258
r_dihedral_angle_4_deg17.669
r_dihedral_angle_3_deg15.684
r_dihedral_angle_1_deg6.091
r_scangle_it4.315
r_scbond_it3.178
r_mcangle_it2.828
r_mcbond_it2.125
r_angle_refined_deg1.568
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.258
r_dihedral_angle_4_deg17.669
r_dihedral_angle_3_deg15.684
r_dihedral_angle_1_deg6.091
r_scangle_it4.315
r_scbond_it3.178
r_mcangle_it2.828
r_mcbond_it2.125
r_angle_refined_deg1.568
r_nbtor_refined0.312
r_symmetry_hbond_refined0.228
r_nbd_refined0.205
r_xyhbond_nbd_refined0.181
r_symmetry_vdw_refined0.133
r_chiral_restr0.109
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2436
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms33

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction