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Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinoic Acid at 1.70 Angstroms Resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 298 0.1 M sodium citrate pH 4.8, 20% PEG 5000 and 10% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.702 α = 90 b = 46.251 β = 90 c = 77.553 γ = 90
Symmetry Space Group P 21 21 21
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 2003-01-12 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 1.000 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 1.7 40 95.6 0.046 17.66 18359 17545 -3 24.6
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) 1.7 1.76 60.5 60.5 0.361 1.91
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 1.7 39.72 17030 17030 1606 93.02 0.151 0.151 0.145 0.1537 0.203 0.2074 RANDOM 21.266
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] -0.12 0.9 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.081 r_dihedral_angle_3_deg 11.589 r_sphericity_free 8.647 r_dihedral_angle_4_deg 7.567 r_dihedral_angle_1_deg 6.753 r_scangle_it 4.479 r_sphericity_bonded 3.618 r_scbond_it 3.179 r_mcangle_it 2.402 r_angle_refined_deg 1.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.081 r_dihedral_angle_3_deg 11.589 r_sphericity_free 8.647 r_dihedral_angle_4_deg 7.567 r_dihedral_angle_1_deg 6.753 r_scangle_it 4.479 r_sphericity_bonded 3.618 r_scbond_it 3.179 r_mcangle_it 2.402 r_angle_refined_deg 1.675 r_rigid_bond_restr 1.641 r_mcbond_it 1.62 r_angle_other_deg 0.811 r_mcbond_other 0.752 r_metal_ion_refined 0.301 r_symmetry_vdw_other 0.23 r_nbd_refined 0.2 r_nbd_other 0.193 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.16 r_symmetry_vdw_refined 0.159 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.093 r_nbtor_other 0.084 r_bond_refined_d 0.017 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 1101 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction