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Crystal structure of human WT NDRG3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 200 mM sodium citrate tribasic dehydrate, 20% PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.341 α = 90 b = 100.15 β = 90.01 c = 110.744 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 ADSC QUANTUM 270 2018-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 2.2 50 99.7 0.101 15.9 5.2 95796
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 2.2 2.24 0.641
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2XMQ 2.2 46.671 88790 4347 92.228 0.169 0.1677 0.1564 0.1848 0.1701 31.604
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] -3.683 -19.234 -5.101 8.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.682 r_dihedral_angle_4_deg 15.101 r_dihedral_angle_3_deg 12.791 r_dihedral_angle_1_deg 6.084 r_lrange_it 3.162 r_lrange_other 3.155 r_angle_other_deg 2.3 r_mcangle_it 1.517 r_mcangle_other 1.516 r_angle_refined_deg 1.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.682 r_dihedral_angle_4_deg 15.101 r_dihedral_angle_3_deg 12.791 r_dihedral_angle_1_deg 6.084 r_lrange_it 3.162 r_lrange_other 3.155 r_angle_other_deg 2.3 r_mcangle_it 1.517 r_mcangle_other 1.516 r_angle_refined_deg 1.143 r_mcbond_it 0.828 r_mcbond_other 0.828 r_scangle_it 0.813 r_scangle_other 0.812 r_scbond_it 0.427 r_scbond_other 0.427 r_nbd_other 0.306 r_symmetry_nbd_refined 0.26 r_symmetry_nbd_other 0.198 r_nbd_refined 0.171 r_xyhbond_nbd_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.162 r_nbtor_refined 0.144 r_symmetry_xyhbond_nbd_other 0.084 r_symmetry_nbtor_other 0.062 r_chiral_restr 0.04 r_bond_other_d 0.036 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13134 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing