☰ Navigation Tabs
Phosphatidylethanolamine-binding protein from Plasmodium vivax
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MAD structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 273 1.0 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 coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.309 α = 90 b = 54.11 β = 90 c = 94.377 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2005-10-29 M SINGLE WAVELENGTH 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9794 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.15 50 96.2 0.098 14.1 3 69478
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.19 84.6 0.233 2 6040
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT MAD structure 1.3 20 44581 2269 88.43 0.161 0.161 0.1654 0.18 0.1837 random 7.04
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] 0.81 0.28 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.83 r_dihedral_angle_4_deg 20.367 r_dihedral_angle_3_deg 13.881 r_dihedral_angle_1_deg 8.286 r_scangle_it 5.881 r_scbond_it 4.621 r_mcangle_it 3.006 r_mcbond_it 2.797 r_angle_refined_deg 1.462 r_angle_other_deg 0.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.83 r_dihedral_angle_4_deg 20.367 r_dihedral_angle_3_deg 13.881 r_dihedral_angle_1_deg 8.286 r_scangle_it 5.881 r_scbond_it 4.621 r_mcangle_it 3.006 r_mcbond_it 2.797 r_angle_refined_deg 1.462 r_angle_other_deg 0.725 r_mcbond_other 0.665 r_symmetry_vdw_refined 0.433 r_symmetry_vdw_other 0.348 r_nbd_refined 0.267 r_nbd_other 0.242 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.184 r_chiral_restr 0.108 r_nbtor_other 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1531 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction