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Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KYH PDB ENTRY 1KYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.005 M ATP, 0.18 M Magnesium Cloride, 13.5%(v/v) PEG 400, 10%(v/v) Glycerol, 0.09 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.92 α = 90 b = 91.92 β = 90 c = 169.63 γ = 90
Symmetry Space Group I 4 2 2
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 210r MIRRORS 2009-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97918 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.51 50 100 0.086 0.086 25.913 7.6 57168 -3 17.3
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 1KYH 1.51 50 57159 2895 99.96 0.135 0.134 0.1456 0.148 0.1572 RANDOM 21.147
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] -0.38 -0.38 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.294 r_dihedral_angle_4_deg 16.15 r_dihedral_angle_3_deg 11.897 r_dihedral_angle_1_deg 6.295 r_scangle_it 4.713 r_angle_other_deg 4.24 r_scbond_it 2.948 r_angle_refined_deg 2.155 r_mcangle_it 1.89 r_mcbond_it 1.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.294 r_dihedral_angle_4_deg 16.15 r_dihedral_angle_3_deg 11.897 r_dihedral_angle_1_deg 6.295 r_scangle_it 4.713 r_angle_other_deg 4.24 r_scbond_it 2.948 r_angle_refined_deg 2.155 r_mcangle_it 1.89 r_mcbond_it 1.043 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2107 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing