☰ Navigation Tabs
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 P1,P3-Di(adenosine-5') triphosphate
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
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.073 α = 90 b = 122.073 β = 90 c = 155.292 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 2.1 50 99.6 0.077 0.077 34.075 11 34349 34168 -3 32.9
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 96.1 0.795 0.795 2.143 5.7
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 2.103 50 34168 1727 99.49 0.159 0.158 0.1652 0.193 0.1951 RANDOM 38.434
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] -0.42 -0.42 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.354 r_dihedral_angle_4_deg 16.953 r_dihedral_angle_3_deg 14.685 r_dihedral_angle_1_deg 6.02 r_scangle_it 4.807 r_angle_other_deg 4.203 r_scbond_it 2.973 r_angle_refined_deg 1.747 r_mcangle_it 1.643 r_mcbond_it 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.354 r_dihedral_angle_4_deg 16.953 r_dihedral_angle_3_deg 14.685 r_dihedral_angle_1_deg 6.02 r_scangle_it 4.807 r_angle_other_deg 4.203 r_scbond_it 2.973 r_angle_refined_deg 1.747 r_mcangle_it 1.643 r_mcbond_it 0.881 r_chiral_restr 0.107 r_bond_refined_d 0.02 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 3777 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 66
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