1V0W

Phospholipase D from Streptomyces sp. strain PMF soaked with the substrate dibutyrylphosphatidylcholine.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.40.2 M NH4AC, 0.1 M CITRATE/ PHOSPHATE BUFFER AT PH5.4, 27.5% PEG 4000. CRYSTALS WERE THEREAFTER BACKSOAKED TWICE IN A PHOSPHATE- FREE BUFFER TO REMOVE TRACE-AMOUNTS OF PHOSPHATE., pH 5.40
Crystal Properties
Matthews coefficientSolvent content
238.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.227α = 90
b = 56.37β = 93.69
c = 68.631γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM1AESRFBM1A

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
11.3519.5990.058.54.789964
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)
11.351.4299.70.34424.5

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 REPLACEMENTTHROUGHOUTBASED ON PDB ENTRY 1F0I1.3519.5899644771990.1620.1610.186RANDOM13.41
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]
-0.62-0.260.550.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.646
r_scangle_it2.982
r_angle_refined_deg1.95
r_scbond_it1.896
r_mcangle_it1.299
r_angle_other_deg0.946
r_mcbond_it0.736
r_nbd_refined0.255
r_nbd_other0.25
r_symmetry_vdw_other0.224
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.646
r_scangle_it2.982
r_angle_refined_deg1.95
r_scbond_it1.896
r_mcangle_it1.299
r_angle_other_deg0.946
r_mcbond_it0.736
r_nbd_refined0.255
r_nbd_other0.25
r_symmetry_vdw_other0.224
r_symmetry_hbond_refined0.216
r_xyhbond_nbd_refined0.154
r_symmetry_vdw_refined0.1
r_nbtor_other0.095
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.008
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3735
Nucleic Acid Atoms
Solvent Atoms626
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
CNSphasing