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Structure of the cAMP responsive exchange factor Epac2 in its auto- inhibited state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O7F PDB ENTRY 1O7F, PDB ENTRY 1BKD experimental model PDB 1BKD PDB ENTRY 1O7F, PDB ENTRY 1BKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100 MM BISTRISPROPANE7.5, 200 MM NANO3, 12% PEG 3350, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.406 α = 90 b = 97.038 β = 90 c = 172.101 γ = 90
Symmetry Space Group P 21 21 21
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 2004-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.7 30 98.6 0.06 23.2 7.3 35428
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 2.7 2.8 96.9 0.3 4.5
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 1O7F, PDB ENTRY 1BKD 2.7 29.88 34014 1791 100 0.248 0.245 0.2417 0.297 0.2918 RANDOM 62.65
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] 0.46 -1.64 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.763 r_dihedral_angle_3_deg 15.602 r_dihedral_angle_4_deg 14.567 r_dihedral_angle_1_deg 4.742 r_angle_refined_deg 0.95 r_scangle_it 0.75 r_mcangle_it 0.608 r_scbond_it 0.44 r_mcbond_it 0.34 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.763 r_dihedral_angle_3_deg 15.602 r_dihedral_angle_4_deg 14.567 r_dihedral_angle_1_deg 4.742 r_angle_refined_deg 0.95 r_scangle_it 0.75 r_mcangle_it 0.608 r_scbond_it 0.44 r_mcbond_it 0.34 r_nbtor_refined 0.292 r_symmetry_hbond_refined 0.218 r_nbd_refined 0.173 r_xyhbond_nbd_refined 0.118 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 7364 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing