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Crystal structure of the inactive form of S-adenosyl-L-homocysteine hydrolase from Thermotoga maritima in binary complex with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 292 0.2 M MgCl2, 0.1 M sodium acetate pH 5.3 and 30% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.9 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.4 α = 90 b = 106.7 β = 109.2 c = 85.9 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 225 mm CCD 2010-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97242 APS 22-BM
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 1.9 30 99.6 0.056 23.4 3.8 80548 -3 26.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93
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 1LI4 1.9 30 79463 1069 99.86 0.16154 0.16108 0.1718 0.19594 0.2057 RANDOM 40.261
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] 1.35 -0.81 0.53 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_4_deg 16.487 r_dihedral_angle_3_deg 13.818 r_long_range_B_refined 7.233 r_long_range_B_other 7.103 r_dihedral_angle_1_deg 6.235 r_scangle_other 4.228 r_mcangle_it 2.874 r_mcangle_other 2.873 r_scbond_it 2.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_4_deg 16.487 r_dihedral_angle_3_deg 13.818 r_long_range_B_refined 7.233 r_long_range_B_other 7.103 r_dihedral_angle_1_deg 6.235 r_scangle_other 4.228 r_mcangle_it 2.874 r_mcangle_other 2.873 r_scbond_it 2.691 r_scbond_other 2.691 r_mcbond_it 1.946 r_mcbond_other 1.945 r_angle_refined_deg 1.583 r_angle_other_deg 0.988 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5877 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing