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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 NADP
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 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.271 α = 90 b = 122.271 β = 90 c = 154.879 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 1.95 50 99.7 0.059 0.059 39.959 9.5 42771 42559 -3 31.1
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 1.98 100 0.717 0.717 2.62 9.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2AX3 1.953 50 42559 2145 99.52 0.16 0.159 0.197 0.1937 RANDOM 37.94
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] -0.59 -0.59 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.545 r_dihedral_angle_4_deg 13.816 r_dihedral_angle_3_deg 13.734 r_dihedral_angle_1_deg 6.067 r_scangle_it 5.26 r_angle_other_deg 4.191 r_scbond_it 3.153 r_mcangle_it 1.919 r_angle_refined_deg 1.69 r_mcbond_it 1.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.545 r_dihedral_angle_4_deg 13.816 r_dihedral_angle_3_deg 13.734 r_dihedral_angle_1_deg 6.067 r_scangle_it 5.26 r_angle_other_deg 4.191 r_scbond_it 3.153 r_mcangle_it 1.919 r_angle_refined_deg 1.69 r_mcbond_it 1.059 r_chiral_restr 0.11 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3829 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 41
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