2GZQ

Phosphatidylethanolamine-binding protein from Plasmodium vivax


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherMAD structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52731.0 ul protein 11 mg/ml 0.4 ul crystallization buffer, 8% PEG8000, 40% PEG 400, 0.04M Hepes, 3.5mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.1542.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.309α = 90
b = 54.11β = 90
c = 94.377γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-10-29MSINGLE WAVELENGTH
21
31
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9794ALS8.2.2

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
11.155096.20.09814.1369478
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)
11.151.1984.60.23326040

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTMAD structure1.32044581226988.430.1610.1610.18random7.04
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]
0.810.28-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.83
r_dihedral_angle_4_deg20.367
r_dihedral_angle_3_deg13.881
r_dihedral_angle_1_deg8.286
r_scangle_it5.881
r_scbond_it4.621
r_mcangle_it3.006
r_mcbond_it2.797
r_angle_refined_deg1.462
r_angle_other_deg0.725
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.83
r_dihedral_angle_4_deg20.367
r_dihedral_angle_3_deg13.881
r_dihedral_angle_1_deg8.286
r_scangle_it5.881
r_scbond_it4.621
r_mcangle_it3.006
r_mcbond_it2.797
r_angle_refined_deg1.462
r_angle_other_deg0.725
r_mcbond_other0.665
r_symmetry_vdw_refined0.433
r_symmetry_vdw_other0.348
r_nbd_refined0.267
r_nbd_other0.242
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.188
r_nbtor_refined0.184
r_chiral_restr0.108
r_nbtor_other0.093
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1531
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction