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Crystal structure of the cGMP-bound GAF a domain from the photoreceptor phosphodiesterase 6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 295 1.5 M ammonium sulfate, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.99 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.598 α = 90 b = 67.598 β = 90 c = 198.533 γ = 120
Symmetry Space Group P 32 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 4r 2006-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97912 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.57 43.85 99.1 0.074 51.8 10.2 17389 17389 -3 57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.66 100 56.5 4.8 9.4 1715
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.57 43.85 17389 17159 860 98.15 0.22245 0.22063 0.2253 0.25705 0.257 RANDOM 68.876
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] 7.33 3.67 7.33 -11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.161 r_dihedral_angle_3_deg 17.936 r_dihedral_angle_4_deg 15.664 r_dihedral_angle_1_deg 6.946 r_mcangle_it 3.907 r_scangle_it 3.623 r_mcbond_it 3.075 r_scbond_it 2.752 r_angle_refined_deg 1.259 r_angle_other_deg 0.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.161 r_dihedral_angle_3_deg 17.936 r_dihedral_angle_4_deg 15.664 r_dihedral_angle_1_deg 6.946 r_mcangle_it 3.907 r_scangle_it 3.623 r_mcbond_it 3.075 r_scbond_it 2.752 r_angle_refined_deg 1.259 r_angle_other_deg 0.813 r_mcbond_other 0.768 r_symmetry_vdw_refined 0.26 r_symmetry_vdw_other 0.244 r_symmetry_hbond_refined 0.226 r_nbd_refined 0.216 r_nbd_other 0.181 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.154 r_nbtor_other 0.083 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2736 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing