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Crystal structure of human NDRG2 protein provides insight into its role as a tumor suppressor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QMQ PDB ENTRY 2QMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 16% PEG 8000, 0.2 M CALCIUM ACETATE, 0.1 M MES (PH 6.8 TO 7.1)
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.232 α = 90 b = 88.049 β = 90 c = 126.907 γ = 90
Symmetry Space Group P 21 21 21
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 PAL/PLS 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 30 97 0.14 11.27 4.6 63329 2
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 2.07 92.2 0.44 1.83 3.1
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 (Observed) 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 PDB ENTRY 2QMQ 2 30 60071 3217 96.45 0.18282 0.18019 0.1954 0.23247 0.2468 RANDOM 28.606
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] -0.45 -0.1 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.103 r_dihedral_angle_4_deg 18.423 r_dihedral_angle_3_deg 15.297 r_dihedral_angle_1_deg 8.966 r_scangle_it 2.9 r_scbond_it 1.845 r_angle_refined_deg 1.342 r_mcangle_it 1.245 r_mcbond_it 0.76 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.103 r_dihedral_angle_4_deg 18.423 r_dihedral_angle_3_deg 15.297 r_dihedral_angle_1_deg 8.966 r_scangle_it 2.9 r_scbond_it 1.845 r_angle_refined_deg 1.342 r_mcangle_it 1.245 r_mcbond_it 0.76 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.276 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6591 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement MOLREP phasing