☰ Navigation Tabs
Crystal structure of the NM23-H2 transcription factor complex with GDP
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 7.5 283 PEG 1500, 50 mM Tris-HCl, 200 mM MgCl2, 2 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.75 α = 90 b = 86.78 β = 90 c = 159.12 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 MAR CCD 165 mm bent Si-mirror 2004-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.1271 APS 14-ID-B
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 1.7 30 96.6 0.062 25.4 6.5 103223 103223
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) 1.7 1.76 81.4 0.33 3.3 4.3
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 1NUE 1.7 30 97878 5172 96.51 0.19811 0.19608 0.1998 0.23592 0.2396 RANDOM 15.833
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] -0.26 0.01 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.997 r_dihedral_angle_4_deg 22.356 r_dihedral_angle_3_deg 14.619 r_dihedral_angle_1_deg 6.638 r_scangle_it 3.011 r_scbond_it 2.166 r_angle_refined_deg 1.669 r_mcangle_it 1.268 r_mcbond_it 1.068 r_angle_other_deg 1.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.997 r_dihedral_angle_4_deg 22.356 r_dihedral_angle_3_deg 14.619 r_dihedral_angle_1_deg 6.638 r_scangle_it 3.011 r_scbond_it 2.166 r_angle_refined_deg 1.669 r_mcangle_it 1.268 r_mcbond_it 1.068 r_angle_other_deg 1.029 r_symmetry_vdw_other 0.29 r_mcbond_other 0.245 r_nbd_refined 0.212 r_nbd_other 0.202 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_refined 0.12 r_chiral_restr 0.106 r_nbtor_other 0.085 r_metal_ion_refined 0.068 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7260 Nucleic Acid Atoms Solvent Atoms 658 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing