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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.
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 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.29 α = 90 b = 122.29 β = 90 c = 155.779 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 ADSC QUANTUM 315 MIRRORS 2009-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97857 APS 19-ID
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 2.2 50 99.8 0.135 0.135 23.626 8.9 30530 30203 -3
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 2.2 2.24 98.2 0.677 0.677 1.772 6.2
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 2.2 50 28561 1515 99.34 0.1638 0.16153 0.1723 0.20642 0.2106 RANDOM 31.85
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] -1.2 -1.2 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.826 r_dihedral_angle_3_deg 15.266 r_dihedral_angle_4_deg 14.188 r_dihedral_angle_1_deg 6.256 r_scangle_it 5.086 r_angle_other_deg 4.179 r_scbond_it 3.097 r_angle_refined_deg 1.853 r_mcangle_it 1.794 r_mcbond_it 0.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.826 r_dihedral_angle_3_deg 15.266 r_dihedral_angle_4_deg 14.188 r_dihedral_angle_1_deg 6.256 r_scangle_it 5.086 r_angle_other_deg 4.179 r_scbond_it 3.097 r_angle_refined_deg 1.853 r_mcangle_it 1.794 r_mcbond_it 0.942 r_chiral_restr 0.105 r_bond_refined_d 0.022 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3773 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 90
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