☰ Navigation Tabs
Crystal structure of a dinucleotide-binding protein (F79A/Y224A/Y246A and deletion of residues 50-75) of ABC transporter (unbound form)
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 sulphate, 0.1M sodium cacodylate pH 6.5, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.93 α = 90 b = 55.47 β = 90 c = 124.4 γ = 90
Symmetry Space Group P 21 21 21
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 2019-12-08 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 2.3 62.2 100 0.15 0.157 0.048 0.997 11.5 10.7 16950
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 2.3 2.38 100 0.559 0.586 0.177 0.928 10.8
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 2.3 62.2 16069 829 99.99 0.1986 0.195 0.1996 0.2695 0.2653 RANDOM 30.045
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] 2.08 -1.77 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.427 r_dihedral_angle_4_deg 22.045 r_dihedral_angle_3_deg 19.85 r_dihedral_angle_1_deg 6.832 r_angle_refined_deg 1.821 r_angle_other_deg 1.37 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.427 r_dihedral_angle_4_deg 22.045 r_dihedral_angle_3_deg 19.85 r_dihedral_angle_1_deg 6.832 r_angle_refined_deg 1.821 r_angle_other_deg 1.37 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2817 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction