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Crystal structure of human NDRG3 I171M/S176H mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6L4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 200 mM ammonium citrate tribasic pH 7.0 and 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.96 37.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.387 α = 90 b = 100.387 β = 90 c = 111.756 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS3 6M 2018-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.97942 PAL/PLS 11C
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 3.3 50 99.3 0.164 14 10.5 10073
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 3.3 3.36 0.629
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 6L4B 3.304 47.006 9141 438 90.05 0.198 0.1961 0.1761 0.2263 0.2138 33.22
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] -8.694 -8.694 17.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.968 r_dihedral_angle_4_deg 15.386 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 6.054 r_lrange_it 5.487 r_lrange_other 5.487 r_mcangle_it 3.282 r_mcangle_other 3.281 r_angle_other_deg 2.319 r_scangle_it 2.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.968 r_dihedral_angle_4_deg 15.386 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 6.054 r_lrange_it 5.487 r_lrange_other 5.487 r_mcangle_it 3.282 r_mcangle_other 3.281 r_angle_other_deg 2.319 r_scangle_it 2.305 r_scangle_other 2.305 r_mcbond_it 1.828 r_mcbond_other 1.827 r_angle_refined_deg 1.279 r_scbond_it 1.226 r_scbond_other 1.226 r_nbd_other 0.33 r_symmetry_nbd_refined 0.278 r_symmetry_nbd_other 0.223 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.133 r_symmetry_nbtor_other 0.064 r_chiral_restr 0.047 r_symmetry_xyhbond_nbd_other 0.044 r_bond_other_d 0.036 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4344 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing