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Crystal structure of a dinucleotide-binding protein (Y224A/Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form I)
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 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2M ammonium phosphate, 0.1M sodium cacodylate pH 6.5, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.63 53.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.52 α = 90 b = 121.69 β = 90.07 c = 65.4 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 2019-07-22 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 1.9 60.84 100 0.157 0.18 0.089 0.969 6.8 4.1 71958
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 1.9 1.94 100 0.57 0.661 0.329 0.692 4
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 1.9 58.52 68415 3510 99.61 0.1649 0.1629 0.1687 0.2044 0.2083 RANDOM 18.485
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] -1.54 -0.4 6.32 -4.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_dihedral_angle_4_deg 19.769 r_dihedral_angle_3_deg 16.012 r_dihedral_angle_1_deg 6.902 r_angle_refined_deg 2.229 r_angle_other_deg 1.527 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.015 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_dihedral_angle_4_deg 19.769 r_dihedral_angle_3_deg 16.012 r_dihedral_angle_1_deg 6.902 r_angle_refined_deg 2.229 r_angle_other_deg 1.527 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.015 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6064 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 166
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction