4QJ4

Structure of a fragment of human phospholipase C-beta3 delta472-569, bound to IP3 and in complex with Galphaq


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OHMPDB ENTRY 3OHM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277.15100 mM BisTris, 200 mM NaCl, 8% (v/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
3.0359.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 201.923α = 90
b = 89.191β = 101.7
c = 92.639γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 300 mm CCD2014-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.979APS21-ID-D

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
13.33085.60.2218.713.72134321289-2000-2
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)
13.33.3664.60.483.272.7

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 3OHM3.329.42027920279101085.140.210630.20780.26665RANDOM72.003
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]
-0.15-0.060.41-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.121
r_dihedral_angle_3_deg14.406
r_dihedral_angle_4_deg13.497
r_dihedral_angle_1_deg5.054
r_long_range_B_refined3.036
r_long_range_B_other3.036
r_mcangle_it1.686
r_mcangle_other1.686
r_scangle_other1.266
r_angle_refined_deg0.929
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.121
r_dihedral_angle_3_deg14.406
r_dihedral_angle_4_deg13.497
r_dihedral_angle_1_deg5.054
r_long_range_B_refined3.036
r_long_range_B_other3.036
r_mcangle_it1.686
r_mcangle_other1.686
r_scangle_other1.266
r_angle_refined_deg0.929
r_mcbond_it0.926
r_mcbond_other0.926
r_angle_other_deg0.676
r_scbond_it0.676
r_scbond_other0.676
r_chiral_restr0.05
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8646
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms59

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing