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Crystal Structure of Rat Odorant Binding Protein 3 (OBP3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A2U PDB ENTRY 2A2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.02 M D-GLUCOSE, 0.02 M D-GALACTOSE, 0.02 M L-FUCOSE, 0.02M D-XYLOSE, 0.02M N-ACETYL-D-GLUCOSAMINE, 0.1 M MORPHEUS BUFFER 1 PH 6.5, 10 % W/V POLYETHYLENE GLYCOL, 20 % POLYETHYLENE GLYCOL 550
Crystal Properties Matthews coefficient Solvent content 2.64 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.98 α = 90 b = 100.53 β = 110.61 c = 72.41 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2012-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 2.8 67.8 95.7 0.13 4.8 1.8 19952 48.8
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 2.8 2.95 95.1 0.48 1.8 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2A2U 2.8 67.776 19938 1025 95.279 0.219 0.2176 0.2202 0.249 0.2488 RANDOM 43.566
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] -2.367 0.698 -0.107 1.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.412 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 14.636 r_dihedral_angle_1_deg 6.423 r_scangle_it 6.185 r_mcangle_it 5.343 r_scbond_it 3.775 r_mcbond_it 3.207 r_mcbond_other 3.207 r_angle_refined_deg 1.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.412 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 14.636 r_dihedral_angle_1_deg 6.423 r_scangle_it 6.185 r_mcangle_it 5.343 r_scbond_it 3.775 r_mcbond_it 3.207 r_mcbond_other 3.207 r_angle_refined_deg 1.371 r_angle_other_deg 0.905 r_nbd_other 0.358 r_nbd_refined 0.197 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.123 r_xyhbond_nbd_other 0.107 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.005 r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5132 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MrBUMP phasing