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Crystal Structure of RBP4 bound to Oleic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QAB PDB ENTRY 1QAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.5 TO 4.2 M NACL, 1M HEPES PH 7.2
Crystal Properties Matthews coefficient Solvent content 3.11 60.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.06 α = 90 b = 103.06 β = 90 c = 72.71 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 105 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.65 50 98.8 0.04 16.96 3.4 34250
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 1.65 1.75 99.8 0.42 2.82 3.2
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 1QAB 1.65 56.34 32522 1727 98.83 0.18924 0.18769 0.1856 0.21919 0.2183 RANDOM 27.401
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] 0.13 0.06 0.13 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.697 r_dihedral_angle_4_deg 19.494 r_dihedral_angle_3_deg 12.372 r_dihedral_angle_1_deg 6.074 r_scangle_it 2.374 r_scbond_it 1.507 r_angle_refined_deg 1.116 r_mcangle_it 0.806 r_mcbond_it 0.501 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.697 r_dihedral_angle_4_deg 19.494 r_dihedral_angle_3_deg 12.372 r_dihedral_angle_1_deg 6.074 r_scangle_it 2.374 r_scbond_it 1.507 r_angle_refined_deg 1.116 r_mcangle_it 0.806 r_mcbond_it 0.501 r_nbtor_refined 0.306 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.189 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined 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_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 1399 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing