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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 NADH
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 58.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.93 α = 90 b = 91.93 β = 90 c = 169.626 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 1.8 50 100 0.083 0.083 45.786 13.4 33796 -3 31.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 99.9 0.896 0.896 1.895 11.8
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 1.8 50 33796 1716 99.91 0.154 0.153 0.1618 0.178 0.1876 RANDOM 36.61
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] -1.49 -1.49 2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.831 r_dihedral_angle_4_deg 16.214 r_dihedral_angle_3_deg 12.283 r_dihedral_angle_1_deg 6.57 r_angle_other_deg 4.221 r_scangle_it 4.175 r_scbond_it 2.645 r_angle_refined_deg 1.757 r_mcangle_it 1.653 r_mcbond_it 0.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.831 r_dihedral_angle_4_deg 16.214 r_dihedral_angle_3_deg 12.283 r_dihedral_angle_1_deg 6.57 r_angle_other_deg 4.221 r_scangle_it 4.175 r_scbond_it 2.645 r_angle_refined_deg 1.757 r_mcangle_it 1.653 r_mcbond_it 0.976 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 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 184 Heterogen Atoms 69
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