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The Structural Identification of the Interaction Site and Functional State of RBP for its Membrane Receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QY0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.9 291 CdCl, malate buffer, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.39 48.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.636 α = 90 b = 53.636 β = 90 c = 137.347 γ = 90
Symmetry Space Group P 43 21 2
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 4 MIRROR 2004-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 42.3 99.8 0.093 0.093 3.8 7.5 27306 27306 15.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.69 100 0.306 0.306 2.4 7.4 3897
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1QY0 1.6 42.3 25898 25898 1372 99.67 0.198 0.198 0.19 0.1938 0.22741 0.2169 RANDOM 19.189
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] 0.43 0.43 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_3_deg 12.898 r_dihedral_angle_4_deg 8.698 r_dihedral_angle_1_deg 6.034 r_scangle_it 3.544 r_scbond_it 2.213 r_mcangle_it 1.477 r_angle_refined_deg 1.224 r_mcbond_it 0.885 r_symmetry_hbond_refined 0.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_3_deg 12.898 r_dihedral_angle_4_deg 8.698 r_dihedral_angle_1_deg 6.034 r_scangle_it 3.544 r_scbond_it 2.213 r_mcangle_it 1.477 r_angle_refined_deg 1.224 r_mcbond_it 0.885 r_symmetry_hbond_refined 0.343 r_nbtor_refined 0.31 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.087 r_metal_ion_refined 0.035 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1184 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling CNS phasing