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Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JBM PDB entry 1JBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 sodium citrate, ammonium acetate, MPD, sodium chloride, pH 5.6,
VAPOR DIFFUSION, HANGING DROP at 293K
Crystal Properties Matthews coefficient Solvent content 2.38 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.254 α = 90 b = 109.956 β = 95.81 c = 83.756 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 2001-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.1000 NSLS X8C
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 1.9 100 97 0.048 25.8 3.8 89378 89378 -1.73 -3 21.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 92.4 0.565 2.3 8488
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 PDB entry 1JBM 1.9 19.79 86242 86242 4364 93.3 0.207 0.207 0.207 0.203 0.25 0.2466 RANDOM 43.5
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] -3.61 -2.79 5.71 -2.11
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_scangle_it 4.15 c_mcangle_it 3.22 c_scbond_it 2.75 c_mcbond_it 2.02 c_angle_deg 1.8 c_improper_angle_d 1.07 c_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8226 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 262
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing CNS refinement