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Crystal structure of a dinucleotide-binding protein 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 4MFI
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 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.16 α = 90 b = 120.88 β = 90 c = 66.06 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 2017-03-23 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 2.15 66.06 98.2 0.105 0.148 0.104 0.987 6.9 2.8 48571
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 2.15 2.21 95.1 0.429 0.594 0.41 0.697 2.5 2.7
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 4MFI 2.15 66.06 46107 2429 97.91 0.1604 0.1582 0.1643 0.2041 0.2091 RANDOM 23.322
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] -6.44 0.66 6.57 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.894 r_dihedral_angle_4_deg 18.788 r_dihedral_angle_3_deg 16.725 r_dihedral_angle_1_deg 6.475 r_angle_refined_deg 1.927 r_angle_other_deg 1.468 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.894 r_dihedral_angle_4_deg 18.788 r_dihedral_angle_3_deg 16.725 r_dihedral_angle_1_deg 6.475 r_angle_refined_deg 1.927 r_angle_other_deg 1.468 r_chiral_restr 0.095 r_bond_refined_d 0.015 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 6084 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 255
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