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Crystal structure of an uncharacterized conserved protein yjbq/upf0047 family, ortholog yugu b.subtilis (ca_c0907) from clostridium acetobutylicum at 1.31 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VMF PDB entry 1VMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 9 277 2.0% Dioxane, 10.0% PEG-20000, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.87 33.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.406 α = 90 b = 79.406 β = 90 c = 50.688 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 Flat mirror 2004-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.31 23.13 96.3 0.072 14.6 5.9 27579 22.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.31 1.38 85.5 0.654 1.7 1.9 3555
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 1VMF 1.31 23.13 26191 1388 96.25 0.15871 0.1574 0.168 0.18503 0.191 RANDOM 15.267
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] -0.03 -0.01 -0.03 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.518 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 12.187 r_dihedral_angle_1_deg 5.497 r_scangle_it 4.714 r_scbond_it 3.291 r_mcangle_it 2.361 r_mcbond_it 1.483 r_angle_refined_deg 1.339 r_angle_other_deg 0.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.518 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 12.187 r_dihedral_angle_1_deg 5.497 r_scangle_it 4.714 r_scbond_it 3.291 r_mcangle_it 2.361 r_mcbond_it 1.483 r_angle_refined_deg 1.339 r_angle_other_deg 0.785 r_mcbond_other 0.452 r_symmetry_vdw_refined 0.36 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.194 r_nbtor_refined 0.176 r_nbd_other 0.171 r_symmetry_vdw_other 0.167 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.097 r_nbtor_other 0.083 r_symmetry_metal_ion_refined 0.066 r_metal_ion_refined 0.062 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 995 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 1
Software Software Software Name Purpose XDS data scaling SCALA data scaling MOLREP phasing REFMAC refinement XDS data reduction CCP4 data scaling