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Human GKRP bound to AMG-5112 and Sorbitol-6-phosphate
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% PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.01 59.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.913 α = 90 b = 148.913 β = 90 c = 132.403 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 2012-05-03 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 2.82 50 94.5 40065 38021 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 2.82 29.59 38021 2006 99.55 0.20241 0.19904 0.2036 0.26609 0.2681 RANDOM 43.24
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 36.509 r_dihedral_angle_4_deg 20.718 r_dihedral_angle_3_deg 18.928 r_long_range_B_refined 7.454 r_long_range_B_other 7.454 r_dihedral_angle_1_deg 6.826 r_mcangle_it 5.041 r_mcangle_other 5.041 r_scangle_other 4.527 r_mcbond_it 3.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.509 r_dihedral_angle_4_deg 20.718 r_dihedral_angle_3_deg 18.928 r_long_range_B_refined 7.454 r_long_range_B_other 7.454 r_dihedral_angle_1_deg 6.826 r_mcangle_it 5.041 r_mcangle_other 5.041 r_scangle_other 4.527 r_mcbond_it 3.097 r_mcbond_other 3.097 r_scbond_it 2.748 r_scbond_other 2.732 r_angle_refined_deg 1.633 r_angle_other_deg 0.86 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 60 Heterogen Atoms 151
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling