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Human dipeptidil peptidase DPP7 complexed with inhibitor GSK237826A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JYH PDB ENTRY 3JYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 300 2M AMMONIUM SULFATE, 0.2M SODIUM ACETATE, 0.1M HEPES, 5% MPD, PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 3.09 60.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.546 α = 90 b = 130.5 β = 102.28 c = 125.075 γ = 90
Symmetry Space Group P 1 21 1
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 2010-05-05 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 Merge 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 2.45 122.213 99.5 0.117 10.4 3.3 92014 50.34
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) 2.45 2.49 99.7 0.793 3.1
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 3JYH 2.45 20.01 91963 4609 0.2206 0.2185 0.231 0.2601 0.2806 RANDOM 41.5
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] 1.9067 -4.9363 -2.652 0.7453
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.74 t_omega_torsion 2.75 t_angle_deg 1.07 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 17.74 t_omega_torsion 2.75 t_angle_deg 1.07 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 13833 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction StructureStudio data collection MOLREP phasing BUSTER refinement