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Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NAD and ATP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AX3 PDB ENTRY 2AX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M Na Cacodylate, 1.6 M Na Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 53.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.399 α = 90 b = 122.399 β = 90 c = 155.122 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 2009-06-11 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 2.1 50 99.5 0.054 0.054 42.952 9 34592 34258 -3 38.8
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 2.1 2.14 98.6 0.745 0.745 2.923 8.2
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 2AX3 2.101 50 34258 1722 99.05 0.171 0.169 0.1755 0.209 0.214 RANDOM 45.939
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.475 r_dihedral_angle_4_deg 14.625 r_dihedral_angle_3_deg 14.174 r_dihedral_angle_1_deg 6.044 r_scangle_it 4.849 r_angle_other_deg 4.206 r_scbond_it 2.891 r_angle_refined_deg 1.763 r_mcangle_it 1.631 r_mcbond_it 0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.475 r_dihedral_angle_4_deg 14.625 r_dihedral_angle_3_deg 14.174 r_dihedral_angle_1_deg 6.044 r_scangle_it 4.849 r_angle_other_deg 4.206 r_scbond_it 2.891 r_angle_refined_deg 1.763 r_mcangle_it 1.631 r_mcbond_it 0.891 r_chiral_restr 0.104 r_bond_refined_d 0.019 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3785 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 96
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