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crystal structure of unliganded PDE5A GAF domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 The unliganded PDE5A (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 277K
Crystal Properties Matthews coefficient Solvent content 4.14 70.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.189 α = 90 b = 144.189 β = 90 c = 134.867 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 2009-06-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791, 0.9796, 0.94, 1.0 NSLS X29A
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 2.8 30 99.8 0.06 19.5 21.6 40247
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) 2.8 2.9 99.3 0.84 4.7
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 MAD THROUGHOUT 2.8 30 38161 2034 99.68 0.24267 0.24042 0.2338 0.28456 0.2754 RANDOM 84.428
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] -1.6 -0.8 -1.6 2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.847 r_dihedral_angle_3_deg 24.919 r_dihedral_angle_4_deg 20.834 r_dihedral_angle_1_deg 12.467 r_scangle_it 8.449 r_scbond_it 5.302 r_mcangle_it 3.79 r_mcbond_it 2.121 r_angle_refined_deg 0.667 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.847 r_dihedral_angle_3_deg 24.919 r_dihedral_angle_4_deg 20.834 r_dihedral_angle_1_deg 12.467 r_scangle_it 8.449 r_scbond_it 5.302 r_mcangle_it 3.79 r_mcbond_it 2.121 r_angle_refined_deg 0.667 r_chiral_restr 0.057 r_gen_planes_refined 0.019 r_bond_refined_d 0.005 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 6110 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling