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Crystal structure of a protein from uncharacterized family UPF0147 from Thermoplasma acidophilum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 2M Ammonium sulfate, 0.1M Tri-HCl pH 7.0, 0.2M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.584 α = 90 b = 50.584 β = 90 c = 59.283 γ = 120
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 2006-12-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931, 0.97949 APS 19-ID
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 1.25 50 98.2 0.099 9.4 11.1 23474 23474 -3 11.8
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) 1.25 1.35 97.3 0.37 3.5 8.9 1515
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.3 24.55 21124 21124 1079 99.62 0.149 0.149 0.147 0.1444 0.178 0.1775 RANDOM 16.124
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] 0.27 0.14 0.27 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.483 r_dihedral_angle_4_deg 18.862 r_dihedral_angle_3_deg 16.334 r_sphericity_free 5.752 r_scangle_it 4.147 r_sphericity_bonded 4.128 r_dihedral_angle_1_deg 4.001 r_scbond_it 3.008 r_mcangle_it 2.05 r_rigid_bond_restr 1.521
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.483 r_dihedral_angle_4_deg 18.862 r_dihedral_angle_3_deg 16.334 r_sphericity_free 5.752 r_scangle_it 4.147 r_sphericity_bonded 4.128 r_dihedral_angle_1_deg 4.001 r_scbond_it 3.008 r_mcangle_it 2.05 r_rigid_bond_restr 1.521 r_angle_refined_deg 1.502 r_mcbond_it 1.359 r_symmetry_hbond_refined 0.301 r_nbd_refined 0.299 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.255 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 875 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building