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Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YVM PDB ENTRY 2YVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.033M MES, 0.053M MAGNESIUM ACETATE, 4.7%(W/V) PEG8000, 6.7%(W/V) GLYCEROL, 10mM AMPCPR, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.679 α = 90 b = 100.748 β = 90 c = 97.369 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2005-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0000 SPring-8 BL44B2
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 1.66 50 97.8 0.041 51.3 5.3 23576 23576 -3 15
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 1.66 1.72 95.8 0.096 14 5.3 2284
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 2YVM 1.66 24.34 23384 23384 2308 96.9 0.188 0.1841 0.204 0.1858 RANDOM 16.8
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] 5.81 -2.48 -3.33
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_angle_deg 2.7 c_improper_angle_d 2.43 c_scangle_it 2.43 c_scbond_it 1.6 c_mcangle_it 1.46 c_mcbond_it 0.91 c_bond_d 0.02
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1437 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 39
Software Software Software Name Purpose MLPHARE phasing CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling