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Crystal structure of the E. coli pyrimidine nucleosidase YeiK bound to a competitive inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q8F PDB ENTRY 1Q8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 100mM Bis-Tris pH 6.5, 45% PPG 500, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.851 α = 90 b = 86.446 β = 98.86 c = 97.817 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 CCD ADSC QUANTUM 4 Silicon crystal 2005-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2 45 97.6 0.08 10.9 3.5 91924 91924 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.11 94.4 0.465 2.9 3.2
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 1Q8F 2 44.97 87302 4601 97.34 0.17523 0.17412 0.1748 0.19587 0.1946 RANDOM 32.102
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] -1.28 0.55 -0.04 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.506 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 13.751 r_dihedral_angle_1_deg 6.01 r_scangle_it 2.745 r_scbond_it 1.685 r_angle_refined_deg 1.422 r_mcangle_it 1.051 r_mcbond_it 0.659 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.506 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 13.751 r_dihedral_angle_1_deg 6.01 r_scangle_it 2.745 r_scbond_it 1.685 r_angle_refined_deg 1.422 r_mcangle_it 1.051 r_mcbond_it 0.659 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.27 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.094 r_metal_ion_refined 0.074 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8988 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms 72
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling