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Crystal structure of the f15w mutant of apo-cellular retinoic acid binding protein type ii at 1.51 angstroms resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 30% (w/v) PEG 4000, 0.2 M Bis-Tris-Propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.582 α = 102 b = 37.03 β = 106.12 c = 58.693 γ = 93
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH 2003-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.000 APS 19-BM
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 1.51 50 92.8 0.032 14.38 42559 39496 16.7
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) 1.51 1.56 75 75 0.261 1.69
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 (All) 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 Rigid body refinement THROUGHOUT 1.51 33.9 35549 35549 3946 92.7 0.18 0.18 0.174 0.1846 0.24 0.2505 RANDOM 18.305
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] -0.53 -0.11 0.2 -1.14 -0.11 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.691 r_dihedral_angle_4_deg 16.907 r_dihedral_angle_3_deg 15.513 r_dihedral_angle_1_deg 6.692 r_sphericity_free 5.639 r_scangle_it 4.557 r_scbond_it 3.071 r_sphericity_bonded 2.934 r_mcangle_it 2.287 r_rigid_bond_restr 1.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.691 r_dihedral_angle_4_deg 16.907 r_dihedral_angle_3_deg 15.513 r_dihedral_angle_1_deg 6.692 r_sphericity_free 5.639 r_scangle_it 4.557 r_scbond_it 3.071 r_sphericity_bonded 2.934 r_mcangle_it 2.287 r_rigid_bond_restr 1.715 r_angle_refined_deg 1.593 r_mcbond_it 1.43 r_angle_other_deg 0.862 r_mcbond_other 0.56 r_metal_ion_refined 0.264 r_symmetry_vdw_refined 0.252 r_symmetry_vdw_other 0.235 r_nbd_refined 0.231 r_nbd_other 0.204 r_xyhbond_nbd_refined 0.203 r_xyhbond_nbd_other 0.198 r_symmetry_hbond_refined 0.182 r_nbtor_refined 0.177 r_chiral_restr 0.102 r_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2047 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction