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Human GKRP bound to AMG-3227 and S6P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LY9 PDB ENTRY 4LY9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M Bis-tris, 0.2M NaI, 16% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.01 59.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.971 α = 90 b = 148.971 β = 90 c = 132.186 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 mirrors 2011-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 2.4 50 97 61379 1
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 4LY9 2.4 39.24 58266 3111 94.34 0.22161 0.21847 0.223 0.28073 0.2797 RANDOM 50.708
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 35.02 r_dihedral_angle_4_deg 19.966 r_dihedral_angle_3_deg 18.105 r_long_range_B_other 8.531 r_long_range_B_refined 8.53 r_dihedral_angle_1_deg 7.027 r_scangle_other 6.329 r_mcangle_it 6.192 r_mcangle_other 6.192 r_scbond_it 4.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.02 r_dihedral_angle_4_deg 19.966 r_dihedral_angle_3_deg 18.105 r_long_range_B_other 8.531 r_long_range_B_refined 8.53 r_dihedral_angle_1_deg 7.027 r_scangle_other 6.329 r_mcangle_it 6.192 r_mcangle_other 6.192 r_scbond_it 4.342 r_scbond_other 4.261 r_mcbond_it 4.191 r_mcbond_other 4.189 r_angle_refined_deg 1.749 r_angle_other_deg 0.888 r_chiral_restr 0.096 r_bond_refined_d 0.015 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 158 Heterogen Atoms 137
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling