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Binding and structural studies of a 5,5-difluoromethyl adenosine nucleoside with the fluorinase enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RQP PDB ENTRY 1RQP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 40% PEG-MME (2K), 0.1 M SODIUM CITRATE PH 4.5 AND 0.12 M AMMONIUM TARTRATE
Crystal Properties Matthews coefficient Solvent content 3.16 61.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.26 α = 90 b = 129.16 β = 90 c = 182.33 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M TOROIDAL MIRROR 2015-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.84 65.67 99.9 0.08 17.2 3.3 77902 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.89 99.2 0.7 2.8 3.3
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 PDB ENTRY 1RQP 1.84 65.67 74202 3933 99.89 0.17915 0.17808 0.1859 0.19983 0.2091 RANDOM 26.602
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.855 r_dihedral_angle_4_deg 14.089 r_dihedral_angle_3_deg 11.435 r_dihedral_angle_1_deg 6.914 r_mcangle_it 2.185 r_scbond_it 1.928 r_angle_refined_deg 1.505 r_mcbond_it 1.397 r_mcbond_other 1.395 r_angle_other_deg 1.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.855 r_dihedral_angle_4_deg 14.089 r_dihedral_angle_3_deg 11.435 r_dihedral_angle_1_deg 6.914 r_mcangle_it 2.185 r_scbond_it 1.928 r_angle_refined_deg 1.505 r_mcbond_it 1.397 r_mcbond_other 1.395 r_angle_other_deg 1.262 r_chiral_restr 0.188 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6659 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing