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Crystal structure of R88A mutant of the NM23-H2 transcription factor
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, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.756 α = 90 b = 104.616 β = 90 c = 118.089 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 bent Si-mirror 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 1.7 26.5 99.8 0.093 16.9 7.2 98113 98113
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 99.4 0.43 3.4 6.9 9666
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 26.5 93076 4899 99.67 0.17589 0.17376 0.181 0.21574 0.2223 RANDOM 14.669
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] -0.37 -0.91 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.793 r_dihedral_angle_4_deg 20.506 r_dihedral_angle_3_deg 14.375 r_dihedral_angle_1_deg 8.059 r_scangle_it 3.849 r_scbond_it 2.706 r_angle_refined_deg 1.72 r_mcangle_it 1.551 r_mcbond_it 1.303 r_angle_other_deg 1.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.793 r_dihedral_angle_4_deg 20.506 r_dihedral_angle_3_deg 14.375 r_dihedral_angle_1_deg 8.059 r_scangle_it 3.849 r_scbond_it 2.706 r_angle_refined_deg 1.72 r_mcangle_it 1.551 r_mcbond_it 1.303 r_angle_other_deg 1.041 r_mcbond_other 0.307 r_symmetry_vdw_other 0.269 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.219 r_nbd_other 0.206 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.172 r_chiral_restr 0.118 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7224 Nucleic Acid Atoms Solvent Atoms 1087 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing