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Crystal structure of the NM23-H2 transcription factor complex with dinucleotide d(AG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUE pdb entry 1NUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 PEG 1500, 50 mM sodium citrate, 20 mM MgCl2, 5 mM DTT, Crystals soaked with 10 mM d(AG), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.92 35.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.466 α = 90 b = 118.219 β = 90 c = 128.91 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 QUANTUM 4 2003-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9000 APS 14-BM-C
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 1.3 27 99.3 0.086 16.4 8 195789
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 1.3 1.35 98.3 0.42 2.3 6.8
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 1NUE 1.3 27 183782 9678 98.2 0.177 0.175 0.1833 0.22 0.2264 RANDOM 14.16
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 0.21 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.612 r_dihedral_angle_4_deg 21.777 r_dihedral_angle_3_deg 13.714 r_sphericity_free 10.771 r_dihedral_angle_1_deg 6.384 r_sphericity_bonded 5.741 r_scangle_it 4.791 r_scbond_it 3.688 r_mcangle_it 2.699 r_rigid_bond_restr 2.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.612 r_dihedral_angle_4_deg 21.777 r_dihedral_angle_3_deg 13.714 r_sphericity_free 10.771 r_dihedral_angle_1_deg 6.384 r_sphericity_bonded 5.741 r_scangle_it 4.791 r_scbond_it 3.688 r_mcangle_it 2.699 r_rigid_bond_restr 2.399 r_mcbond_it 2.265 r_angle_refined_deg 1.885 r_mcbond_other 1.237 r_angle_other_deg 1.202 r_nbd_refined 0.227 r_nbd_other 0.215 r_symmetry_vdw_other 0.21 r_chiral_restr 0.187 r_nbtor_refined 0.187 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.137 r_nbtor_other 0.084 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7218 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing