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Crystal structure of a dinucleotide-binding protein (F79A) 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 MICROBATCH 6.5 277 0.2M ammonium phosphate, 0.1M sodium cacodylate pH6.5, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.39 α = 90 b = 121.58 β = 90 c = 66.19 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 2019-01-07 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 1.77 60.79 95.4 0.116 0.13 0.058 0.991 9.3 4.6 85038
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 1.77 1.8 86.7 0.574 0.655 0.308 0.706 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7C0F 1.77 60.79 80749 4254 95.1 0.1449 0.143 0.1823 0.2005 RANDOM 20.289
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] -5.34 0.03 11.92 -6.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.718 r_dihedral_angle_4_deg 18.027 r_dihedral_angle_3_deg 14.713 r_dihedral_angle_1_deg 6.531 r_angle_refined_deg 2.286 r_angle_other_deg 1.542 r_chiral_restr 0.124 r_bond_refined_d 0.018 r_gen_planes_refined 0.016 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.718 r_dihedral_angle_4_deg 18.027 r_dihedral_angle_3_deg 14.713 r_dihedral_angle_1_deg 6.531 r_angle_refined_deg 2.286 r_angle_other_deg 1.542 r_chiral_restr 0.124 r_bond_refined_d 0.018 r_gen_planes_refined 0.016 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6099 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms 164
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