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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 NADPH 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 2.56 51.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.943 α = 90 b = 120.943 β = 90 c = 154.802 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 MARMOSAIC 225 mm CCD BERYLLIUM LENSES 2010-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.6 50 94.4 0.079 0.079 23.69 10 17945 16834 -3 60.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 91 1.844 10
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 2.605 50 16834 871 93.84 0.166 0.162 0.1687 0.237 0.2417 RANDOM 53.586
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] 0.34 0.34 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.148 r_dihedral_angle_3_deg 18.069 r_dihedral_angle_4_deg 14.602 r_dihedral_angle_1_deg 6.404 r_angle_other_deg 4.167 r_scangle_it 3.98 r_scbond_it 2.481 r_angle_refined_deg 1.974 r_mcangle_it 1.368 r_mcbond_it 0.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.148 r_dihedral_angle_3_deg 18.069 r_dihedral_angle_4_deg 14.602 r_dihedral_angle_1_deg 6.404 r_angle_other_deg 4.167 r_scangle_it 3.98 r_scbond_it 2.481 r_angle_refined_deg 1.974 r_mcangle_it 1.368 r_mcbond_it 0.693 r_chiral_restr 0.098 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3773 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 118
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