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Crystal structure of Aplysia cyclase complexed with substrate NGD and product cGDPR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R12 PDB ENTRY 1R12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M IMIDAZOLE, PH 7.5, 12-14% PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.84 56.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.494 α = 90 b = 57.852 β = 100.94 c = 71.303 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 100 CCD ADSC CCD 2009-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 NSRRC BL13B1
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 1.8 30 94 0.08 17.5 3.4 48804 1.4 27.2
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 1.8 1.86 69.4 0.55 1.4
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 PDB ENTRY 1R12 1.8 25 46173 2484 94.13 0.17914 0.17631 0.1757 0.23278 0.2314 RANDOM 29.843
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] -0.13 -1.1 -0.38 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.653 r_dihedral_angle_4_deg 20.227 r_dihedral_angle_3_deg 14.963 r_dihedral_angle_1_deg 5.984 r_scangle_it 5.222 r_scbond_it 3.331 r_angle_refined_deg 2.071 r_mcangle_it 2.049 r_mcbond_it 1.2 r_chiral_restr 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.653 r_dihedral_angle_4_deg 20.227 r_dihedral_angle_3_deg 14.963 r_dihedral_angle_1_deg 5.984 r_scangle_it 5.222 r_scbond_it 3.331 r_angle_refined_deg 2.071 r_mcangle_it 2.049 r_mcbond_it 1.2 r_chiral_restr 0.178 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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_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 4039 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing