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Crystal structure of PDE5A GAF domain (89-518)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 The unliganded PDE5A1C149S (20 mg/mL) was crystallized by vapor diffusion against the well buffer of 10% PEG3350, 5% MPD, 0.1 M sodium citrate, pH5.6, 20 mM DTT. , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.17 70.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.534 α = 90 b = 144.534 β = 90 c = 135.008 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC QUANTUM 315 M MAD 2 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.08 NSLS X29A 2
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 3.1 30 100 0.128 9.5 11 29794
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.1 3.2 100 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.1 30 28228 1507 99.48 0.23505 0.23219 0.2231 0.28865 0.2817 RANDOM 100.54
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] -1.69 -0.85 -1.69 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.389 r_dihedral_angle_3_deg 27.946 r_dihedral_angle_4_deg 21.659 r_dihedral_angle_1_deg 14.257 r_scangle_it 8.826 r_scbond_it 5.417 r_mcangle_it 4.224 r_mcbond_it 2.334 r_angle_refined_deg 1.319 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.389 r_dihedral_angle_3_deg 27.946 r_dihedral_angle_4_deg 21.659 r_dihedral_angle_1_deg 14.257 r_scangle_it 8.826 r_scbond_it 5.417 r_mcangle_it 4.224 r_mcbond_it 2.334 r_angle_refined_deg 1.319 r_chiral_restr 0.106 r_gen_planes_refined 0.023 r_bond_refined_d 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5921 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling