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Crystal structure of human NDRG3 C30S 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 295 200 mM sodium citrate tribasic dehydrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.88 57.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.759 α = 90 b = 99.759 β = 90 c = 332.71 γ = 120
Symmetry Space Group P 31 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 2018-12-04 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) Rrim I (All) Rpim I (All) 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 3.4 50 97.7 0.103 0.111 0.039 6.4 6.6 26798
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.46 97.5 0.732 0.787 0.275 0.826 6.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6L4B 3.4 47.824 26570 1332 96.992 0.243 0.2415 0.238 0.2774 0.2726 RANDOM 121.104
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] -1.134 -0.567 -1.134 3.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.621 r_dihedral_angle_3_deg 13.709 r_dihedral_angle_4_deg 13.419 r_dihedral_angle_1_deg 6.677 r_lrange_it 4.888 r_lrange_other 4.888 r_mcangle_it 3.433 r_mcangle_other 3.433 r_scangle_it 2.866 r_scangle_other 2.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.621 r_dihedral_angle_3_deg 13.709 r_dihedral_angle_4_deg 13.419 r_dihedral_angle_1_deg 6.677 r_lrange_it 4.888 r_lrange_other 4.888 r_mcangle_it 3.433 r_mcangle_other 3.433 r_scangle_it 2.866 r_scangle_other 2.866 r_angle_other_deg 2.296 r_mcbond_it 1.906 r_mcbond_other 1.906 r_scbond_it 1.627 r_scbond_other 1.627 r_angle_refined_deg 1.246 r_symmetry_xyhbond_nbd_refined 0.284 r_symmetry_nbd_refined 0.248 r_symmetry_nbd_other 0.226 r_nbd_refined 0.225 r_nbd_other 0.221 r_symmetry_xyhbond_nbd_other 0.175 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.154 r_symmetry_nbtor_other 0.063 r_chiral_restr 0.046 r_bond_other_d 0.036 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8670 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing