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Mutant structure of methyltransferase from Streptomyces hygroscopicus
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 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.871 α = 90 b = 97.136 β = 90 c = 135.234 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 MX300HE 2013-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A 1.0 NSRRC BL15A
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 2.1 30 99.9 43121 43121 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 2.1 2.18 100
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 2.1 29.06 2 43121 43121 2310 95.27 0.14663 0.14395 0.1558 0.1958 0.2021 RANDOM 27.368
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] -0.03 0.07 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.447 r_dihedral_angle_4_deg 16.754 r_dihedral_angle_3_deg 15.094 r_long_range_B_refined 7.881 r_long_range_B_other 7.522 r_dihedral_angle_1_deg 7.367 r_scangle_other 5.488 r_scbond_it 3.632 r_scbond_other 3.631 r_mcangle_it 3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.447 r_dihedral_angle_4_deg 16.754 r_dihedral_angle_3_deg 15.094 r_long_range_B_refined 7.881 r_long_range_B_other 7.522 r_dihedral_angle_1_deg 7.367 r_scangle_other 5.488 r_scbond_it 3.632 r_scbond_other 3.631 r_mcangle_it 3.21 r_mcangle_other 3.207 r_mcbond_it 2.294 r_mcbond_other 2.293 r_angle_refined_deg 1.946 r_angle_other_deg 0.924 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5182 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 114
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling