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Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, soaked with GTP
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 CRYSTALLIZATION: 50 MM NA-CITRATE PH 3.5 & 30 % PEG 3000, SOAKING: 50 MM NA-CITRATE PH 3.5, 35 % PEG 1500 & 20 MM GTP FOR 3 H
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.89 α = 90 b = 46.43 β = 90 c = 106.49 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 MARRESEARCH MAR165 MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M) 2010-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
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 2.05 25 99.9 0.08 15.66 6.9 13618 -3 34.44
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 2.05 2.1 100 1.08 2.18 6.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2XMI 2.05 19.946 1.99 13608 681 99.99 0.2041 0.2017 0.1947 0.2483 0.2346 48.91
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] 3.7421 -5.8502 2.1082
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.265 f_angle_d 0.762 f_chiral_restr 0.05 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1688 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing