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Rat Phosphatidylethanolamine-Binding Protein Containing the S153E Mutation in the Complex with o-Phosphorylethanolamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BD9 PDB ENTRY 1BD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 277 10mM o-phosphorylethamine+ 2mM GTP crystallized in 0.1M Sodium Acetate trihydrate pH 4.5 and 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 4.50
Crystal Properties Matthews coefficient Solvent content 2.05 40.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.971 α = 90 b = 57.211 β = 109.69 c = 80.886 γ = 90
Symmetry Space Group P 1 21 1
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 SBC-2 MIRRORS 2003-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.2 32.25 99.2 0.123 3.1 3.7 25715
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) 2.21 2.29 94.1 0.276 1.8 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BD9 2.2 32.24 24400 22343 2419 96.35 0.18957 0.18192 0.1766 0.26104 0.2534 RANDOM 14.515
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] -0.67 0.45 0.13 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.11 r_dihedral_angle_3_deg 13.471 r_dihedral_angle_4_deg 13.3 r_mcangle_it 8.464 r_mcbond_it 5.765 r_dihedral_angle_1_deg 4.296 r_scangle_it 3.918 r_scbond_it 2.44 r_angle_refined_deg 1.374 r_symmetry_vdw_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.11 r_dihedral_angle_3_deg 13.471 r_dihedral_angle_4_deg 13.3 r_mcangle_it 8.464 r_mcbond_it 5.765 r_dihedral_angle_1_deg 4.296 r_scangle_it 3.918 r_scbond_it 2.44 r_angle_refined_deg 1.374 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4367 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling EPMR phasing