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Crystal structure of a dinucleotide-binding protein (Q274A) 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 2.65 53.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.2 α = 90 b = 58.29 β = 94.78 c = 121.9 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 2019-04-20 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 2.4 66.06 100 0.242 0.278 0.136 0.951 6.4 4.1 36616
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 2.4 2.49 100 0.585 0.674 0.332 0.714 4.1
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 2.4 66.06 34821 1778 99.98 0.2305 0.2274 0.2937 0.2818 RANDOM 21.787
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] -0.24 0.24 -1.37 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 17.509 r_dihedral_angle_1_deg 6.935 r_angle_refined_deg 1.72 r_angle_other_deg 1.276 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 17.509 r_dihedral_angle_1_deg 6.935 r_angle_refined_deg 1.72 r_angle_other_deg 1.276 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 317 Heterogen Atoms 109
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