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Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 20% PEG 4000, 10% isopropanol, 0.1 M Tris-HCl pH 8.0, 2 mM adenosine, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.21 44.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.417 α = 90 b = 122.417 β = 90 c = 126.571 γ = 90
Symmetry Space Group P 43 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 MAR CCD 165 mm 2007-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.17 20 99.9 0.057 38.3 10.7 319469 -3 9.9
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 1.17 1.19 98.5 0.708 2.3 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT R FREE 1V8B 1.17 20 319641 315006 1093 98.9 0.128 0.128 0.159 0.1533 RANDOM 11.94
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] -0.13 -0.13 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_4_deg 16.458 r_dihedral_angle_3_deg 12.702 r_sphericity_free 9.999 r_dihedral_angle_1_deg 6.595 r_scangle_it 5.564 r_sphericity_bonded 5.036 r_scbond_it 4.085 r_mcangle_it 2.643 r_angle_refined_deg 1.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_4_deg 16.458 r_dihedral_angle_3_deg 12.702 r_sphericity_free 9.999 r_dihedral_angle_1_deg 6.595 r_scangle_it 5.564 r_sphericity_bonded 5.036 r_scbond_it 4.085 r_mcangle_it 2.643 r_angle_refined_deg 1.926 r_rigid_bond_restr 1.905 r_mcbond_it 1.881 r_angle_other_deg 1.232 r_mcbond_other 0.968 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7516 Nucleic Acid Atoms Solvent Atoms 1493 Heterogen Atoms 152
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling