☰ Navigation Tabs
Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N58 PDB entry 3N58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 292 0.2 M ammonium acetate, pH 7.1, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.72 α = 90 b = 176.47 β = 90 c = 104.27 γ = 90
Symmetry Space Group P 21 21 2
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 RAYONIX MX-225 mirrors 2011-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.74 47.85 98.7 0.086 12.34 6.37 203245 200550 -3
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 1.74 1.79 97 0.694 1.95
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 R-FREE PDB entry 3N58 1.74 47.85 203245 199538 1011 100 0.14775 0.14763 0.1538 0.17222 0.1727 RANDOM 21.592
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 -0.07 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.013 r_dihedral_angle_4_deg 15.545 r_dihedral_angle_3_deg 13.317 r_dihedral_angle_1_deg 6.02 r_scangle_it 4.115 r_scbond_it 2.568 r_angle_refined_deg 1.618 r_mcangle_it 1.599 r_angle_other_deg 0.961 r_mcbond_it 0.907
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.013 r_dihedral_angle_4_deg 15.545 r_dihedral_angle_3_deg 13.317 r_dihedral_angle_1_deg 6.02 r_scangle_it 4.115 r_scbond_it 2.568 r_angle_refined_deg 1.618 r_mcangle_it 1.599 r_angle_other_deg 0.961 r_mcbond_it 0.907 r_mcbond_other 0.283 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_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 14468 Nucleic Acid Atoms Solvent Atoms 1704 Heterogen Atoms 338
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction PHASER phasing