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Crystal structure of NDX2 in complex with MG2+ from thermus thermophilus HB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.05M MES, 0.08M MAGNESIUM ACETATE, 7%(W/V) PEG8000, 10%(W/V) GLYCEROL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.763 α = 90 b = 101.176 β = 90 c = 97.492 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 2004-10-28 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RIGAKU JUPITER 210 2004-11-17 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0000 SPring-8 BL44B2 2 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.03985, 1.03940, 1.00000 SPring-8 BL26B2
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 1.7 50 99.9 0.044 48 7 22707 -3 15.3
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 1.7 1.76 99.8 0.239 7 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.7 25.99 22599 20354 2245 99.9 0.205 0.2068 0.225 0.2098 RANDOM 19.1
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] 6.03 -2.14 -3.89
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_scangle_it 2.33 c_mcangle_it 1.66 c_angle_deg 1.6 c_scbond_it 1.53 c_improper_angle_d 1.14 c_mcbond_it 1 c_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1437 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 2
Software Software Software Name Purpose MLPHARE phasing CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling