3H4W

Structure of a Ca+2 dependent Phosphatidylinositol-specific phospholipase C (PI-PLC) Enzyme from Streptomyces antibioticus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.627721% PEG 10000, 85mM sodium acetate pH 4.6, 170mM ammonium acetate, 9% glycerol. SeMe-derived crystals obtained with initial microseeding with underivatized crystals followed by a series of macroseedings with derivatized enzyme and same conditions., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2846.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.377α = 90
b = 155.172β = 90
c = 41.409γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2008-01-01SAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9796SSRLBL9-2

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
11.577.6195.150.0588.268911.6552173521713.713.6
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)
1.51.5881.660.223.195.766345

Refinement

Statistics
Diffraction IDStructure Solution 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 DIFFRACTIONSAD1.577.5952168523494.730.1850.1840.2RANDOM14.295
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]
1.12-0.61-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.275
r_dihedral_angle_4_deg11.859
r_dihedral_angle_3_deg10.883
r_dihedral_angle_1_deg5.111
r_sphericity_free2.344
r_scangle_it2.19
r_sphericity_bonded1.674
r_scbond_it1.591
r_angle_refined_deg0.995
r_mcangle_it0.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.275
r_dihedral_angle_4_deg11.859
r_dihedral_angle_3_deg10.883
r_dihedral_angle_1_deg5.111
r_sphericity_free2.344
r_scangle_it2.19
r_sphericity_bonded1.674
r_scbond_it1.591
r_angle_refined_deg0.995
r_mcangle_it0.981
r_rigid_bond_restr0.877
r_mcbond_it0.567
r_chiral_restr0.068
r_bond_refined_d0.005
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2411
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms49

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SHELXDphasing