☰ Navigation Tabs
Crystal structure of a dinucleotide-binding protein (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 = 58.8 α = 90 b = 104.39 β = 90 c = 65.74 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 2019-07-14 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 2.2 65.74 97.9 0.174 0.197 0.091 0.978 7.1 4.4 39359
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 2.2 2.27 95.9 0.511 0.585 0.282 0.778 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7C0F 2.2 65.74 37323 2010 97.62 0.1903 0.1878 0.1917 0.2378 0.2403 RANDOM 20.675
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] -13.2 3.87 29.19 -15.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.65 r_dihedral_angle_4_deg 18.258 r_dihedral_angle_3_deg 17.889 r_dihedral_angle_1_deg 7.675 r_angle_refined_deg 2.03 r_angle_other_deg 1.336 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.65 r_dihedral_angle_4_deg 18.258 r_dihedral_angle_3_deg 17.889 r_dihedral_angle_1_deg 7.675 r_angle_refined_deg 2.03 r_angle_other_deg 1.336 r_chiral_restr 0.092 r_bond_refined_d 0.013 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 6038 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 90
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