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Catalytic Domain Of Human Phosphodiesterase 5A in Complex with GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T9R PDB ENTRY 1T9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 PEG 4000, lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.969 α = 90 b = 90.872 β = 98.07 c = 68.991 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 93 CCD ADSC QUANTUM 210 2003-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
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 69.01 99.8 0.124 6.4 3.8 48496 48496
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 2.052 99.9 0.558 2.8 3.8 3719
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1T9R 2 69.01 48496 48496 2561 99.8 0.17712 0.17527 0.186 0.21235 0.2215 RANDOM 8.597
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] 0.69 0.36 -0.53 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.702 r_scangle_it 2.519 r_scbond_it 1.554 r_angle_refined_deg 1.352 r_mcangle_it 0.842 r_angle_other_deg 0.81 r_mcbond_it 0.42 r_symmetry_vdw_other 0.283 r_nbd_other 0.222 r_nbd_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 2.702 r_scangle_it 2.519 r_scbond_it 1.554 r_angle_refined_deg 1.352 r_mcangle_it 0.842 r_angle_other_deg 0.81 r_mcbond_it 0.42 r_symmetry_vdw_other 0.283 r_nbd_other 0.222 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.156 r_symmetry_vdw_refined 0.128 r_nbtor_other 0.085 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 5274 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection ELVES data scaling EPMR phasing