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Crystal Structure of the R132K:R111L:L121E Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.50 Angstroms Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FS6 PDB ENTRY 2FS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 30% (w/v) PEG 4000, 0.1 M Bis-TRIS Propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 46.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.553 α = 73.4 b = 37.22 β = 73.7 c = 61.058 γ = 89.73
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 2006-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 1.00 APS 32-ID
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 1.5 55.9 96.1 0.043 8.3 42526 42526 19.6
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) 1.5 1.55 93 0.2976 2.4
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 2FS6 1.5 55.9 41632 4167 93.23 0.161 0.154 0.1573 0.227 0.2289 RANDOM 24.517
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] 0.07 -0.25 0.13 -1.26 -0.11 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.712 r_dihedral_angle_4_deg 14.219 r_dihedral_angle_3_deg 13.252 r_sphericity_free 10.321 r_scangle_it 7.634 r_sphericity_bonded 7.085 r_dihedral_angle_1_deg 6.434 r_scbond_it 5.318 r_mcangle_it 3.848 r_rigid_bond_restr 3.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.712 r_dihedral_angle_4_deg 14.219 r_dihedral_angle_3_deg 13.252 r_sphericity_free 10.321 r_scangle_it 7.634 r_sphericity_bonded 7.085 r_dihedral_angle_1_deg 6.434 r_scbond_it 5.318 r_mcangle_it 3.848 r_rigid_bond_restr 3.213 r_mcbond_it 2.639 r_angle_refined_deg 2.325 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.173 r_metal_ion_refined 0.149 r_symmetry_hbond_refined 0.143 r_bond_refined_d 0.028 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction AUTOMAR data reduction