2AR5

Crystal structure of the mammalian C2alpha-PI3 Kinase PX-domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OCSPDB ENTRY 1OCS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
162930.1M Maleic acid/NaOH, 10% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.8556.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.554α = 90
b = 56.554β = 90
c = 92.894γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98CCDADSC QUANTUM 42004-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.848.899.20.0575.41636541.2
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)
11.81.8699.90.492.2

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1OCS1.848.8163451551982699.20.2230.2220.244RANDOM42.75
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]
0.520.260.52-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg13.55
r_scangle_it5.969
r_mcangle_it3.982
r_scbond_it3.853
r_mcbond_it2.293
r_angle_refined_deg1.89
r_angle_other_deg0.979
r_symmetry_vdw_other0.352
r_nbd_refined0.271
r_nbd_other0.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg13.55
r_scangle_it5.969
r_mcangle_it3.982
r_scbond_it3.853
r_mcbond_it2.293
r_angle_refined_deg1.89
r_angle_other_deg0.979
r_symmetry_vdw_other0.352
r_nbd_refined0.271
r_nbd_other0.257
r_symmetry_vdw_refined0.249
r_xyhbond_nbd_refined0.177
r_chiral_restr0.143
r_nbtor_other0.093
r_symmetry_hbond_refined0.05
r_bond_refined_d0.016
r_gen_planes_other0.016
r_gen_planes_refined0.015
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms957
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing