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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 9% PEG 8000, 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE (PH 6.4 TO 7.5).
Crystal Properties Matthews coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.411 α = 90 b = 88.897 β = 90 c = 126.799 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
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 2.81 40 99.6 0.1 19.1 6.6 24361 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 2.8 2.9 99 0.42 4.5 6.3
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 2.81 40 23070 1242 99.19 0.2039 0.20095 0.2011 0.25847 0.2547 RANDOM 41.372
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] -0.11 -1.11 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.244 r_dihedral_angle_4_deg 25.877 r_dihedral_angle_3_deg 21.222 r_dihedral_angle_1_deg 9.456 r_scangle_it 3.501 r_scbond_it 2.371 r_angle_refined_deg 2.332 r_mcangle_it 1.833 r_mcbond_it 1.114 r_nbtor_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.244 r_dihedral_angle_4_deg 25.877 r_dihedral_angle_3_deg 21.222 r_dihedral_angle_1_deg 9.456 r_scangle_it 3.501 r_scbond_it 2.371 r_angle_refined_deg 2.332 r_mcangle_it 1.833 r_mcbond_it 1.114 r_nbtor_refined 0.338 r_symmetry_vdw_refined 0.324 r_symmetry_hbond_refined 0.316 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.137 r_bond_refined_d 0.029 r_gen_planes_refined 0.008 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 6615 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOLREP phasing