☰ Navigation Tabs
Crystal structure of a dinucleotide-binding protein (Y56F) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C0F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 277 0.2M ammonium phosphate, 0.1M sodium cacodylate pH6.5, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.6 α = 90 b = 58.45 β = 95.1 c = 123.09 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 100 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2019-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 61.3 97.2 0.139 0.159 0.076 0.978 7.8 4.3 62323
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 92.4 0.467 0.531 0.249 0.832 4.2
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 7C0F 2 61.3 59216 3088 97.19 0.1815 0.1792 0.1869 0.2267 0.2315 RANDOM 20.931
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] -9.26 -1.84 -5.86 15.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.053 r_dihedral_angle_4_deg 19.283 r_dihedral_angle_3_deg 15.168 r_dihedral_angle_1_deg 6.309 r_angle_refined_deg 1.956 r_angle_other_deg 1.475 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.053 r_dihedral_angle_4_deg 19.283 r_dihedral_angle_3_deg 15.168 r_dihedral_angle_1_deg 6.309 r_angle_refined_deg 1.956 r_angle_other_deg 1.475 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6120 Nucleic Acid Atoms Solvent Atoms 656 Heterogen Atoms 141
Software Software Software Name Purpose HKL-3000 data reduction MOSFLM data reduction Aimless data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction