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Crystal structure of human soluble adenylyl cyclase in complex with alpha,beta-methyleneadenosine-5'-triphosphate and the allosteric inhibitor LRE1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CLK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 100 mM sodium acetate pH 4.8
200 mM tri-sodium-citrate
15% (w/v) PEG 4000
10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.032 α = 90 b = 100.032 β = 90 c = 98.658 γ = 120
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 DECTRIS PILATUS 6M 2015-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
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 1.86 44.61 99.9 0.122 10.2 4.6 46795
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 1.86 1.98 99.7 1.281 1.3 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4clk 1.86 44.61 44694 2101 99.88 0.17806 0.17594 0.1845 0.22308 0.225 RANDOM 34.4
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] 0.33 0.16 0.33 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 14.928 r_long_range_B_refined 8.75 r_long_range_B_other 8.748 r_dihedral_angle_1_deg 6.833 r_scangle_other 6.394 r_mcangle_it 4.797 r_mcangle_other 4.796 r_scbond_it 4.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 14.928 r_long_range_B_refined 8.75 r_long_range_B_other 8.748 r_dihedral_angle_1_deg 6.833 r_scangle_other 6.394 r_mcangle_it 4.797 r_mcangle_other 4.796 r_scbond_it 4.29 r_scbond_other 4.28 r_mcbond_it 3.296 r_mcbond_other 3.295 r_angle_refined_deg 2.035 r_angle_other_deg 1.063 r_chiral_restr 0.128 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3608 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing