5FYO

Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, crystal form 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H4W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP10PEG3350 24-27%, CAPS/BICINE MIX PH 9.0-10 GRID, BEST CRYSTALS CLOSER TO PH 10, SEEDING FROM PACT H4 (0.2M KSCN, 20% PEG3350, BIS TRIS PROPANE PH 8.5), ORYX ROBOT, 24 WELL PLATE, HANGING DROPS
Crystal Properties
Matthews coefficientSolvent content
238.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.08α = 90
b = 96.08β = 90
c = 113.34γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.548.8199.90.0527.512.9851922

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3H4W1.548.8180756438199.940.126910.124740.16673RANDOM23.65
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]
0.440.44-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.158
r_dihedral_angle_2_deg35.202
r_dihedral_angle_4_deg16.374
r_sphericity_bonded16.194
r_dihedral_angle_3_deg11.233
r_dihedral_angle_1_deg6.329
r_mcangle_it3.413
r_scbond_it3.397
r_mcbond_it2.93
r_mcbond_other2.926
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.158
r_dihedral_angle_2_deg35.202
r_dihedral_angle_4_deg16.374
r_sphericity_bonded16.194
r_dihedral_angle_3_deg11.233
r_dihedral_angle_1_deg6.329
r_mcangle_it3.413
r_scbond_it3.397
r_mcbond_it2.93
r_mcbond_other2.926
r_rigid_bond_restr2.605
r_angle_refined_deg1.575
r_angle_other_deg1.287
r_chiral_restr0.132
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4603
Nucleic Acid Atoms
Solvent Atoms469
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing