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Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with cordycepin
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 cordycepin, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.22 44.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.623 α = 90 b = 122.623 β = 90 c = 126.622 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 MARMOSAIC 225 mm CCD 2009-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12
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 50 99.7 0.131 17.5 10.5 65547 -3 22.7
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 2 2.07 100 0.686 3.1 9.5
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 1V8B 2 50 65729 64344 1119 99.8 0.157 0.156 0.1651 0.201 0.2083 RANDOM 18.72
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] -0.11 -0.11 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.935 r_dihedral_angle_4_deg 17.579 r_dihedral_angle_3_deg 13.944 r_dihedral_angle_1_deg 6.278 r_scangle_it 5.427 r_scbond_it 3.576 r_angle_refined_deg 1.479 r_mcangle_it 1.434 r_angle_other_deg 1.236 r_mcbond_it 0.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.935 r_dihedral_angle_4_deg 17.579 r_dihedral_angle_3_deg 13.944 r_dihedral_angle_1_deg 6.278 r_scangle_it 5.427 r_scbond_it 3.576 r_angle_refined_deg 1.479 r_mcangle_it 1.434 r_angle_other_deg 1.236 r_mcbond_it 0.756 r_mcbond_other 0.184 r_chiral_restr 0.084 r_bond_refined_d 0.015 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7500 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 134
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling