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X-Ray Structure of a Cytosolic 5'-Nucleotidase III from Mus Musculus MM.158936
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 10 MG/ML PROTEIN, 26% PEG 8K, 0.10 M MOPS (HEPES USED AS CRYOPROTECTANT), pH 7.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3 58.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.674 α = 90 b = 133.674 β = 90 c = 38.889 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 300 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97911 APS 22-ID
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 2.35 43.755 98.5 0.091 6.818 5.4 31917
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 2.35 2.4 87.8 87.8 0.367 2.067 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2.35 43.755 31910 1619 98.503 0.1659 0.16588 0.163 0.1764 0.2198 0.2363 RANDOM 48.154
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] 0.303 0.151 0.303 -0.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.957 r_dihedral_angle_4_deg 23.413 r_dihedral_angle_3_deg 16.224 r_dihedral_angle_1_deg 6.439 r_scangle_it 6.275 r_scbond_it 4.645 r_mcangle_it 2.414 r_angle_refined_deg 1.548 r_mcbond_it 1.379 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.957 r_dihedral_angle_4_deg 23.413 r_dihedral_angle_3_deg 16.224 r_dihedral_angle_1_deg 6.439 r_scangle_it 6.275 r_scbond_it 4.645 r_mcangle_it 2.414 r_angle_refined_deg 1.548 r_mcbond_it 1.379 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.107 r_bond_refined_d 0.019 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4652 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction PHENIX phasing SHELXD phasing SOLOMON phasing ARP/wARP model building