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Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, complexed with sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XMI PDB ENTRY 2XMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.5 50MM NA-CITRATE PH 3.5, 2.9M AMMONIUM SULFATE, 10% PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.33 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.43 α = 90 b = 82.43 β = 90 c = 86.31 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 CCD MARMOSAIC 225 mm CCD 2009-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 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 2.1 35 99.8 0.04 19.98 3.85 38236 -3
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 2.1 2.15 99.8 0.56 2.5 3.83
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 2XMI 2.1 71.4 36254 1981 99.76 0.19162 0.18971 0.2221 0.2275 0.2596 RANDOM 71.987
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] 30.58 30.58 -61.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.387 r_dihedral_angle_4_deg 22.379 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 6.667 r_scangle_it 4.705 r_scbond_it 3.391 r_mcangle_it 2.609 r_mcbond_it 1.668 r_angle_refined_deg 1.554 r_angle_other_deg 1.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.387 r_dihedral_angle_4_deg 22.379 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 6.667 r_scangle_it 4.705 r_scbond_it 3.391 r_mcangle_it 2.609 r_mcbond_it 1.668 r_angle_refined_deg 1.554 r_angle_other_deg 1.097 r_mcbond_other 0.481 r_symmetry_hbond_refined 0.287 r_symmetry_vdw_refined 0.255 r_symmetry_vdw_other 0.249 r_nbd_refined 0.212 r_nbtor_refined 0.185 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.125 r_xyhbond_nbd_other 0.103 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other 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 4977 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing