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Mutant structure of methyltransferase from Streptomyces hygroscopicus complexed with S-adenosyl-L-homocysteine and methylphenylpyruvic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 16% PEG3350, 0.2M sodium iodine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.16 α = 90 b = 89.626 β = 90 c = 136.622 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 100 CCD RAYONIX MX225HE 2012-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 30 99.9 24097 24097 2 2
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 2.5 2.59 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 THROUGHOUT 4KIB 2.5 29.34 2 24097 24097 1290 99.09 0.18216 0.17831 0.1809 0.25476 0.2581 RANDOM 52.145
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] 1.67 2.32 -3.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.793 r_dihedral_angle_4_deg 18.275 r_dihedral_angle_3_deg 16.447 r_long_range_B_refined 7.749 r_long_range_B_other 7.708 r_dihedral_angle_1_deg 6.008 r_scangle_other 4.971 r_mcangle_it 4.376 r_mcangle_other 4.376 r_scbond_it 3.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.793 r_dihedral_angle_4_deg 18.275 r_dihedral_angle_3_deg 16.447 r_long_range_B_refined 7.749 r_long_range_B_other 7.708 r_dihedral_angle_1_deg 6.008 r_scangle_other 4.971 r_mcangle_it 4.376 r_mcangle_other 4.376 r_scbond_it 3.031 r_scbond_other 3.029 r_mcbond_it 2.834 r_mcbond_other 2.833 r_angle_refined_deg 1.38 r_angle_other_deg 0.786 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5246 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 112
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling