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Rat Phosphatidylethanolamine-Binding Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IQX PDB ENTRY 2IQX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2M Cacl2, HEPES pH 7.5 and 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.93 36.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.694 α = 90 b = 70.588 β = 109.96 c = 38.672 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-3 mirrors 2006-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 1.4 26.23 89.3 0.042 13.6 3.9 28140 28140
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) 1.4 1.45 48.2 0.103 7.45 2.5 1510
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 (All) 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 2IQX 1.4 26.23 25281 25281 2838 89.31 0.15321 0.15321 0.14879 0.1535 0.19299 0.1976 RANDOM 12.223
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] -0.29 -0.07 0.26 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.718 r_dihedral_angle_3_deg 13.602 r_dihedral_angle_4_deg 12.947 r_dihedral_angle_1_deg 6.284 r_scangle_it 2.799 r_scbond_it 1.969 r_angle_refined_deg 1.458 r_mcangle_it 1.363 r_mcbond_it 0.821 r_nbd_refined 0.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.718 r_dihedral_angle_3_deg 13.602 r_dihedral_angle_4_deg 12.947 r_dihedral_angle_1_deg 6.284 r_scangle_it 2.799 r_scbond_it 1.969 r_angle_refined_deg 1.458 r_mcangle_it 1.363 r_mcbond_it 0.821 r_nbd_refined 0.264 r_xyhbond_nbd_refined 0.237 r_symmetry_hbond_refined 0.236 r_symmetry_vdw_refined 0.194 r_chiral_restr 0.105 r_metal_ion_refined 0.049 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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_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 1686 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing