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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 Acetyl Coenzyme A
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 2.63 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.507 α = 90 b = 122.507 β = 90 c = 154.904 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 2009-10-16 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 1.95 50 93.9 0.074 0.074 26.048 8.9 43273 40598 -3 24
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 1.95 1.98 94.9 0.776 0.776 2.292 7.6
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 1.95 50 40471 2035 93.84 0.158 0.157 0.1662 0.192 0.2026 RANDOM 30.406
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] -0.7 -0.7 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.368 r_dihedral_angle_4_deg 14.887 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_1_deg 5.96 r_scangle_it 5.146 r_angle_other_deg 4.296 r_scbond_it 3.029 r_angle_refined_deg 1.821 r_mcangle_it 1.798 r_mcbond_it 0.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.368 r_dihedral_angle_4_deg 14.887 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_1_deg 5.96 r_scangle_it 5.146 r_angle_other_deg 4.296 r_scbond_it 3.029 r_angle_refined_deg 1.821 r_mcangle_it 1.798 r_mcbond_it 0.978 r_chiral_restr 0.246 r_bond_refined_d 0.02 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 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 193 Heterogen Atoms 83
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