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STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN SOLUBLE GUANYLATE CYCLASE 1 BETA 3.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ET6 PDB ENTRY 3ET6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 PROTEIN WAS CONCENTRATED TO 12 MG/ML IN PURIFICATION BUFFER (10MM HEPES, 500MM NACL, 5% GLYCEROL, 10% GALACTOSE, 0.5MM TCEP)AND SET UP IN SITTING DROP IN A 1:2 RATIO WITH HAMPTON INDEX SCREEN - B8 (1.4M TRI-SODIUM CITRATE DIHYDRATE, 0.1M HEPES, PH 7.5).
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.59 α = 90 b = 90.38 β = 90 c = 140.03 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD ADSC CCD 2009-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.63 37 99.3 0.06 9.9 3.4 49220 1.3 19.6
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 1.63 1.67 99.8 0.56 2.1 3.5
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 PDB ENTRY 3ET6 1.63 37 49220 2637 99.3 0.18536 0.18352 0.1998 0.21922 0.2307 RANDOM 12.388
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] -0.07 0.31 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.954 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 14.659 r_scangle_it 12.01 r_scbond_it 8.715 r_dihedral_angle_1_deg 5.849 r_mcangle_it 5.452 r_mcbond_it 3.742 r_angle_refined_deg 1.585 r_angle_other_deg 1.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.954 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 14.659 r_scangle_it 12.01 r_scbond_it 8.715 r_dihedral_angle_1_deg 5.849 r_mcangle_it 5.452 r_mcbond_it 3.742 r_angle_refined_deg 1.585 r_angle_other_deg 1.238 r_mcbond_other 1.131 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3056 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing