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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 in complex with ADP
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 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.309 α = 90 b = 122.309 β = 90 c = 155.312 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 SBC-3 MIRRORS 2008-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97857 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 2.15 50 99 0.095 0.095 20.724 7.9 251926 251926 -3 33.5
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 2.15 2.19 96.2 0.839 0.839 1.986 7.1
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 2.15 35.42 31868 1617 98.78 0.163 0.161 0.1685 0.197 0.2009 RANDOM 37.85
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] -0.47 -0.47 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.691 r_dihedral_angle_3_deg 15.214 r_dihedral_angle_4_deg 14.045 r_dihedral_angle_1_deg 6.179 r_scangle_it 4.68 r_angle_other_deg 4.21 r_scbond_it 2.82 r_angle_refined_deg 1.748 r_mcangle_it 1.554 r_mcbond_it 0.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.691 r_dihedral_angle_3_deg 15.214 r_dihedral_angle_4_deg 14.045 r_dihedral_angle_1_deg 6.179 r_scangle_it 4.68 r_angle_other_deg 4.21 r_scbond_it 2.82 r_angle_refined_deg 1.748 r_mcangle_it 1.554 r_mcbond_it 0.821 r_chiral_restr 0.102 r_bond_refined_d 0.019 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3778 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 89
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