4Q6X

Structure of phospholipase D Beta1B1i from Sicarius terrosus venom at 2.14 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RLHPDB ENTRY 3RLH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52983 mg/ml protein, 12% PEG 3350, 0.1M Bis-Tris, 0.1M magnesium chloride , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8433.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.222α = 90
b = 49.222β = 90
c = 90.114γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.127SSRLBL7-1

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
12.1438.5699.10.07713.93.71335213352-329.7
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)
12.142.2594.80.4362.631828

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3RLH2.1438.56133251267465199.140.166890.166890.164150.22069RANDOM39.122
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]
0.340.340.34-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.936
r_dihedral_angle_4_deg15.933
r_dihedral_angle_3_deg13.837
r_dihedral_angle_1_deg6.692
r_long_range_B_refined4.454
r_long_range_B_other4.416
r_scangle_other3.142
r_mcangle_it2.547
r_mcangle_other2.546
r_scbond_it1.964
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.936
r_dihedral_angle_4_deg15.933
r_dihedral_angle_3_deg13.837
r_dihedral_angle_1_deg6.692
r_long_range_B_refined4.454
r_long_range_B_other4.416
r_scangle_other3.142
r_mcangle_it2.547
r_mcangle_other2.546
r_scbond_it1.964
r_scbond_other1.964
r_mcbond_it1.679
r_mcbond_other1.679
r_angle_refined_deg1.386
r_angle_other_deg0.766
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2240
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms1

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling