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Crystal structure of the protein TM0936 from Thermotoga maritima complexed with ZN and S-inosylhomocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J6P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 3.5 Sodium formate, 0.5 mM Zinc Chloride , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.24 62.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.278 α = 90 b = 113.278 β = 90 c = 80.298 γ = 120
Symmetry Space Group P 32 2 1
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 4 mirrors 2006-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97915 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 25 91.7 0.049 7.3 32035 32035 19.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1J6P 2.1 24.53 32035 32035 1575 91.7 0.212 0.209 0.209 0.2093 0.238 0.2378 RANDOM 37.1
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] -8.33 -3.56 -8.33 16.66
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 2.9 c_scbond_it 2 c_mcangle_it 1.81 c_angle_deg 1.3 c_mcbond_it 1.18 c_improper_angle_d 0.79 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3209 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 27
Software Software Software Name Purpose CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing