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Human GKRP bound to AMG-5980 and S6P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Internal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 Well buffer: 0.1M Bis-tris, 0.2M NaI, 16% PEG 8K, pH 7.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.03 59.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.129 α = 90 b = 149.129 β = 90 c = 132.383 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 100 CCD RIGAKU SATURN 92 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 26 93.9 77422 72687 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 Internal structure 2.2 26 1 77422 72687 3826 90.34 0.23263 0.22977 0.2357 0.28816 0.2873 RANDOM 50.834
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.172 r_dihedral_angle_4_deg 20.158 r_dihedral_angle_3_deg 18.436 r_long_range_B_refined 8.16 r_long_range_B_other 8.16 r_dihedral_angle_1_deg 7.248 r_scangle_other 6.352 r_mcangle_it 6.047 r_mcangle_other 6.047 r_scbond_it 4.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.172 r_dihedral_angle_4_deg 20.158 r_dihedral_angle_3_deg 18.436 r_long_range_B_refined 8.16 r_long_range_B_other 8.16 r_dihedral_angle_1_deg 7.248 r_scangle_other 6.352 r_mcangle_it 6.047 r_mcangle_other 6.047 r_scbond_it 4.491 r_scbond_other 4.397 r_mcbond_it 4.287 r_mcbond_other 4.285 r_angle_refined_deg 1.879 r_angle_other_deg 0.911 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9075 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 142
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling