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phosphodiesterase-9A in complex with inhibitor 4b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 3.0M Na formate, 0.1M HEPES (pH 7.5), 5% xylitol
Crystal Properties Matthews coefficient Solvent content 2.91 57.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.467 α = 90 b = 103.467 β = 90 c = 268.921 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL RIGAKU HyPix-3000 2021-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54056
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 2.7 23.5321 98.4 0.14 21.4 8.9 40355 34.5489656212
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 2.7 2.8 100 0.45 5 9.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 6A3N 2.70000890032 23.5320777477 2.02616478662 40354 1961 98.4003901487 0.27379037353 0.270818453015 0.2731 0.333696578959 0.3329 30.0805812221
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.5496245342 f_angle_d 1.21122133664 f_chiral_restr 0.0575645343453 f_bond_d 0.010211549722 f_plane_restr 0.00768188660648
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5192 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing