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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 AMP
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 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.102 α = 90 b = 122.102 β = 90 c = 155.614 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 300 mm CCD MIRRORS 2008-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12712 APS 21-ID-D
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 2.4 50 99.8 0.07 0.07 38.523 8.7 200896 200896 -3 58.9
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 2.4 2.44 98.9 0.938 0.938 1.814 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 2.4 50 23145 1193 99.49 0.17 0.167 0.1722 0.216 0.2194 RANDOM 58.275
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] -0.83 -0.83 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.863 r_dihedral_angle_4_deg 16.037 r_dihedral_angle_3_deg 15.562 r_dihedral_angle_1_deg 6.329 r_scangle_it 4.222 r_angle_other_deg 4.22 r_scbond_it 2.533 r_angle_refined_deg 1.706 r_mcangle_it 1.471 r_mcbond_it 0.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.863 r_dihedral_angle_4_deg 16.037 r_dihedral_angle_3_deg 15.562 r_dihedral_angle_1_deg 6.329 r_scangle_it 4.222 r_angle_other_deg 4.22 r_scbond_it 2.533 r_angle_refined_deg 1.706 r_mcangle_it 1.471 r_mcbond_it 0.752 r_chiral_restr 0.096 r_bond_refined_d 0.02 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 3773 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 47
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