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Human DPP4 in complex with ligand 34n
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.27-0.30 M sodium acetate 17-18% polyethylene glycol 3350 0.1 M tris hydrochloride pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.03 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.125 α = 90 b = 126.008 β = 90 c = 137.546 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 100 IMAGE PLATE RIGAKU RAXIS HTC 2010-12-22 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) 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 2.61 137.546 99.9 0.124 6.18 5.2 63311 45.23
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 2.61 2.67 100 0.494 1.6 5.1
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 FOURIER SYNTHESIS THROUGHOUT 1X70 2.61 92.91 62926 3168 99.78 0.152 0.1481 0.1509 0.2259 0.2274 RANDOM 28.67
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] 8.3479 -5.1307 -3.2171
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.77 t_omega_torsion 3.23 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.77 t_omega_torsion 3.23 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11966 Nucleic Acid Atoms Solvent Atoms 1387 Heterogen Atoms 1762
Software Software Software Name Purpose BUSTER refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing