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Crystal structure of s-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with 5-methylthiotubericidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other S.AUREUS MTAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 30% PEG MME 5000, 0.1M MES, 0.2M AMMONIUM SULPHATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.01 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.735 α = 90 b = 72.345 β = 90 c = 116.246 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV++ MIRRORS 2008-04-20 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.5418
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 1.45 20.62 87.5 0.033 27.3 4.4 66215 66215 13.91
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 1.45 1.48 21.3 0.247 2.4 1.5
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 (All) 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 S.AUREUS MTAN 1.45 20.47 66215 62797 3357 87.63 0.1636 0.1636 0.16181 0.1582 0.19744 0.1949 RANDOM 15.251
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.834 r_dihedral_angle_3_deg 12.99 r_dihedral_angle_4_deg 11.138 r_dihedral_angle_1_deg 6.385 r_angle_refined_deg 2.314 r_chiral_restr 0.157 r_bond_refined_d 0.025 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3538 Nucleic Acid Atoms Solvent Atoms 785 Heterogen Atoms 20
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling