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Crystal structure of Cordyceps militaris IDCase D323A mutant in complex with 5-carboxyl-uracil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop 8.5 289 25% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, sitting drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.98 37.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.266 α = 90 b = 54.301 β = 121.04 c = 143.776 γ = 90
Symmetry Space Group C 1 2 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 RAYONIX MX225HE 2013-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
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 50 99.7 0.077 10.1 3.6 74453
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 2.18 99.5 0.267 3.5 7378
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 4HK5 2.1 47.96 74452 3750 99.06 0.1772 0.1749 0.1871 0.2202 0.228 RANDOM 31.1058
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] 1.95 1.69 -2.09 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.441 r_sphericity_free 25.703 r_dihedral_angle_4_deg 14.905 r_dihedral_angle_3_deg 13.786 r_dihedral_angle_1_deg 4.993 r_rigid_bond_restr 4.173 r_sphericity_bonded 3.199 r_mcangle_it 1.054 r_angle_refined_deg 1.017 r_mcbond_it 0.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.441 r_sphericity_free 25.703 r_dihedral_angle_4_deg 14.905 r_dihedral_angle_3_deg 13.786 r_dihedral_angle_1_deg 4.993 r_rigid_bond_restr 4.173 r_sphericity_bonded 3.199 r_mcangle_it 1.054 r_angle_refined_deg 1.017 r_mcbond_it 0.913 r_mcbond_other 0.913 r_angle_other_deg 0.848 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11241 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 176
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHENIX phasing