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Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B0V PDB ENTRY 2B0V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 283 0.1 M Citric acid pH 4.0, 3.5% w/v PEG 4000, 0.064 M Magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.96 α = 90 b = 70.521 β = 103.3 c = 145.031 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 2008-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A Photon Factory BL-6A
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 2.69 50 98.8 0.093 18.8 2.9 37388 1
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) 2.69 2.8 99.7 0.245 5.9 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2B0V 2.69 33.56 37999 35479 1865 98.3 0.196 0.193 0.1937 0.27 0.269 RANDOM 28.13
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] -0.05 0.27 0.14 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.386 r_dihedral_angle_3_deg 20.542 r_dihedral_angle_4_deg 18.912 r_dihedral_angle_1_deg 7.048 r_scangle_it 3.327 r_scbond_it 2.082 r_angle_refined_deg 1.848 r_mcangle_it 1.533 r_mcbond_it 0.92 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.386 r_dihedral_angle_3_deg 20.542 r_dihedral_angle_4_deg 18.912 r_dihedral_angle_1_deg 7.048 r_scangle_it 3.327 r_scbond_it 2.082 r_angle_refined_deg 1.848 r_mcangle_it 1.533 r_mcbond_it 0.92 r_nbtor_refined 0.324 r_symmetry_vdw_refined 0.272 r_nbd_refined 0.248 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 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_refined 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 9645 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing