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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 2.23 44.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.009 α = 90 b = 90.219 β = 90 c = 136.505 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 ADSC QUANTUM 315r 2012-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97 NSRRC BL13C1
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 2.3 30 100 30264 30264 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 2.3 2.38 100
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 2.3 27.94 2 30264 30264 1616 99.53 0.16494 0.16157 0.1676 0.22745 0.2307 RANDOM 35.26
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] 1.75 0.17 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.976 r_dihedral_angle_4_deg 17.336 r_dihedral_angle_3_deg 16.023 r_long_range_B_refined 5.962 r_long_range_B_other 5.891 r_dihedral_angle_1_deg 5.654 r_scangle_other 4.095 r_mcangle_it 2.882 r_mcangle_other 2.881 r_scbond_it 2.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.976 r_dihedral_angle_4_deg 17.336 r_dihedral_angle_3_deg 16.023 r_long_range_B_refined 5.962 r_long_range_B_other 5.891 r_dihedral_angle_1_deg 5.654 r_scangle_other 4.095 r_mcangle_it 2.882 r_mcangle_other 2.881 r_scbond_it 2.518 r_scbond_other 2.518 r_mcbond_it 1.896 r_mcbond_other 1.896 r_angle_refined_deg 1.415 r_angle_other_deg 0.811 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5232 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 109
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling