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Crystal structure of human NDRG1
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, SITTING DROP 285.15 1.4 M sodium malonate (pH 6.25), 10 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.57 α = 90 b = 108.57 β = 90 c = 119.33 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M-F 2020-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.9762 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.96 48.55 95.66 0.98 4.33 4.26 14800 63.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.96 3.07 0.76 1.42
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2XMQ 2.96 48.55 1.34 14733 733 95.71 0.2699 0.2685 0.2679 0.2946 0.2911 65.42
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.0322 f_angle_d 0.5765 f_chiral_restr 0.0454 f_plane_restr 0.0035 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3861 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing