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Structure of hypothetical molybdenum cofactor biosynthesis protein B from Sulfolobus tokodaii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y5E PDB ENTRY 1y5e
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDER OIL 7 298 10% W/V PEG 8000, 0.1M TRIS-HCL, 0.2M MGCL2, pH 7.0, MICROBATCH UNDER OIL, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 4.79 74.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.675 α = 90 b = 136.675 β = 90 c = 210.525 γ = 120
Symmetry Space Group P 64 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 MARMOSAIC 225 mm CCD mirrors 2007-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.074 SRS PX10.1
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 30 98.5 0.065 9 91510 91510 31
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 1.9 1.97 97.7 0.61 0.5 2 4 8758
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 1y5e 1.9 29.74 85236 89742 4506 98.16 0.16936 0.16936 0.16841 0.1747 0.18695 0.1917 RANDOM 47.856
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.48 r_dihedral_angle_3_deg 12.912 r_dihedral_angle_4_deg 11.021 r_dihedral_angle_1_deg 5.622 r_scangle_it 2.865 r_scbond_it 2.195 r_angle_refined_deg 1.477 r_mcangle_it 1.234 r_mcbond_it 1.087 r_angle_other_deg 0.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.48 r_dihedral_angle_3_deg 12.912 r_dihedral_angle_4_deg 11.021 r_dihedral_angle_1_deg 5.622 r_scangle_it 2.865 r_scbond_it 2.195 r_angle_refined_deg 1.477 r_mcangle_it 1.234 r_mcbond_it 1.087 r_angle_other_deg 0.997 r_symmetry_vdw_refined 0.249 r_symmetry_vdw_other 0.225 r_nbd_refined 0.211 r_mcbond_other 0.205 r_symmetry_hbond_refined 0.197 r_nbd_other 0.191 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.172 r_metal_ion_refined 0.125 r_chiral_restr 0.093 r_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3882 Nucleic Acid Atoms Solvent Atoms 581 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection