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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 8 289 1M ammonium phosphate dibasic, 0.1M imidazole, 0.2M sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.53 51.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.737 α = 90 b = 85.737 β = 90 c = 118.806 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 315 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) 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 2.3 63 99.9 22054 22050 1 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 30 20882 1128 99.94 0.23265 0.23116 0.234 0.26072 0.2625 RANDOM 31.782
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] 0.35 0.18 0.35 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.745 r_dihedral_angle_3_deg 11.482 r_dihedral_angle_4_deg 11.233 r_dihedral_angle_1_deg 4.429 r_long_range_B_refined 2.19 r_long_range_B_other 2.19 r_angle_refined_deg 1.138 r_angle_other_deg 0.621 r_mcangle_it 0.541 r_mcangle_other 0.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.745 r_dihedral_angle_3_deg 11.482 r_dihedral_angle_4_deg 11.233 r_dihedral_angle_1_deg 4.429 r_long_range_B_refined 2.19 r_long_range_B_other 2.19 r_angle_refined_deg 1.138 r_angle_other_deg 0.621 r_mcangle_it 0.541 r_mcangle_other 0.541 r_scangle_other 0.337 r_mcbond_it 0.288 r_mcbond_other 0.288 r_scbond_it 0.171 r_scbond_other 0.171 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 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 2822 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 176
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling