☰ Navigation Tabs
Crystal structure of a dinucleotide-binding protein (Y224A/Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form II)
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 pH 6.5, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.28 46.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.31 α = 90 b = 58.84 β = 93.1 c = 103.58 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 2019-07-19 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 58.84 99.7 0.12 0.136 0.065 0.98 11 4.4 77250
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 1.81 96 0.271 0.313 0.152 0.911 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 1.77 57.25 73355 3877 99.62 0.1833 0.1813 0.1907 0.2217 0.2271 RANDOM 21.656
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] -0.71 -0.32 -1.22 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.458 r_dihedral_angle_4_deg 17.977 r_dihedral_angle_3_deg 14.519 r_dihedral_angle_1_deg 6.135 r_angle_refined_deg 1.892 r_angle_other_deg 1.506 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.458 r_dihedral_angle_4_deg 17.977 r_dihedral_angle_3_deg 14.519 r_dihedral_angle_1_deg 6.135 r_angle_refined_deg 1.892 r_angle_other_deg 1.506 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6066 Nucleic Acid Atoms Solvent Atoms 742 Heterogen Atoms 118
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