7LM2 | pdb_00007lm2

HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 3C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherpreviously derived model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29312-14% PEG6000, 100 MM MES/NAOH, PH 5.75, 5 MM DTT
Crystal Properties
Matthews coefficientSolvent content
2.753.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.284α = 90
b = 109.308β = 90
c = 142.579γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.99998SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
12.7986.751000.0580.0665.58.336279
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.793.0199.90.5890.6731.38.2

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-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpreviously derived model2.7986.753546273999.970.24150.24050.230.28950.28RANDOM97.127
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]
0.641.81-2.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.314
r_dihedral_angle_4_deg13.153
r_dihedral_angle_3_deg12.816
r_dihedral_angle_1_deg5.389
r_angle_other_deg1.272
r_angle_refined_deg1.042
r_nbd_refined0.161
r_nbtor_refined0.155
r_nbd_other0.136
r_symmetry_hbond_refined0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.314
r_dihedral_angle_4_deg13.153
r_dihedral_angle_3_deg12.816
r_dihedral_angle_1_deg5.389
r_angle_other_deg1.272
r_angle_refined_deg1.042
r_nbd_refined0.161
r_nbtor_refined0.155
r_nbd_other0.136
r_symmetry_hbond_refined0.132
r_symmetry_vdw_other0.108
r_symmetry_vdw_refined0.093
r_xyhbond_nbd_refined0.074
r_nbtor_other0.068
r_chiral_restr0.058
r_bond_refined_d0.008
r_bond_other_d0.002
r_gen_planes_refined0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9029
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction