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Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine 3'-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O8N PDB ENTRY 2O8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1 M SODIUM ACETATE, 1.5 M AMMONIUM SULFATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.094 α = 90 b = 126.094 β = 90 c = 110.962 γ = 120
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 2008-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.04399 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.05 50 99.8 0.061 0.061 38.741 5.6 119546 119546 -3 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 99.4 0.361 0.361 3.203 3.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2O8N 2.05 50 21270 1089 99.3 0.18 0.179 0.201 0.1981 RANDOM 55.107
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] -4.54 -2.27 -4.54 6.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.64 r_dihedral_angle_4_deg 17.589 r_dihedral_angle_3_deg 15.567 r_dihedral_angle_1_deg 6.372 r_scangle_it 4.238 r_angle_other_deg 4.042 r_scbond_it 2.885 r_angle_refined_deg 1.752 r_mcangle_it 1.658 r_mcbond_it 0.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.64 r_dihedral_angle_4_deg 17.589 r_dihedral_angle_3_deg 15.567 r_dihedral_angle_1_deg 6.372 r_scangle_it 4.238 r_angle_other_deg 4.042 r_scbond_it 2.885 r_angle_refined_deg 1.752 r_mcangle_it 1.658 r_mcbond_it 0.971 r_chiral_restr 0.11 r_bond_refined_d 0.021 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1808 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing