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Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with a non-retinoid ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 1 M ammonium phosphate dibasic, 0.1 M imidazole, pH 8.0, 200 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.23 61.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.531 α = 90 b = 96.531 β = 90 c = 118.072 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 ADSC QUANTUM 315r 2007-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.4 83.63 99.9 0.065 0.065 9.6 6.8 24454 24453 1 1.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 100 0.42 1.8 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 30 24417 23158 1243 99.94 0.24409 0.24184 0.2445 0.28691 0.284 RANDOM 44.631
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] 0.7 0.35 0.7 -2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.564 r_dihedral_angle_4_deg 13.887 r_dihedral_angle_3_deg 12.402 r_dihedral_angle_1_deg 5.974 r_long_range_B_refined 4.259 r_long_range_B_other 4.218 r_mcangle_it 2.165 r_mcangle_other 2.165 r_scangle_other 2.025 r_mcbond_it 1.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.564 r_dihedral_angle_4_deg 13.887 r_dihedral_angle_3_deg 12.402 r_dihedral_angle_1_deg 5.974 r_long_range_B_refined 4.259 r_long_range_B_other 4.218 r_mcangle_it 2.165 r_mcangle_other 2.165 r_scangle_other 2.025 r_mcbond_it 1.214 r_mcbond_other 1.214 r_scbond_it 1.127 r_scbond_other 1.127 r_angle_refined_deg 1.089 r_angle_other_deg 0.65 r_chiral_restr 0.061 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2830 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 144
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling