☰ Navigation Tabs
Crystal structure of NudC domain-containing protein 2 (13542905) from Mus musculus at 1.95 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 277 NANODROP, 0.2M NaNO3, 20.0% PEG 3350, No Buffer pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.568 α = 74.51 b = 64.504 β = 81.06 c = 64.423 γ = 81.22
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 Adjustable focusing mirrors in K-B geometry 2007-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97942 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 29.148 95.5 0.096 0.096 3.1 2.9 47221 25.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2 94.2 0.607 0.607 0.8 2.9 3450
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 (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 1.95 29.148 47101 2394 95.33 0.192 0.19 0.1981 0.235 0.2414 RANDOM 28.349
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] -0.35 0.8 1.24 -0.86 1.88 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.194 r_dihedral_angle_3_deg 14.272 r_dihedral_angle_4_deg 13.768 r_scangle_it 7.946 r_scbond_it 5.49 r_dihedral_angle_1_deg 5.11 r_mcangle_it 3.508 r_mcbond_it 2.69 r_angle_refined_deg 1.61 r_angle_other_deg 0.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.194 r_dihedral_angle_3_deg 14.272 r_dihedral_angle_4_deg 13.768 r_scangle_it 7.946 r_scbond_it 5.49 r_dihedral_angle_1_deg 5.11 r_mcangle_it 3.508 r_mcbond_it 2.69 r_angle_refined_deg 1.61 r_angle_other_deg 0.896 r_mcbond_other 0.295 r_symmetry_vdw_other 0.276 r_nbd_refined 0.214 r_nbd_other 0.195 r_symmetry_hbond_refined 0.193 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_refined 0.116 r_chiral_restr 0.099 r_nbtor_other 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4227 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing