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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 54.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.989 α = 90 b = 96.81 β = 90 c = 135.404 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 30 99.9 48442 48442 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 2.07 100
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4KIB 2 29.05 2 48442 48442 2605 92.95 0.15506 0.15204 0.21062 0.2114 RANDOM 30.337
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] 0.34 -0.1 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.193 r_dihedral_angle_4_deg 19.012 r_dihedral_angle_3_deg 15.97 r_long_range_B_refined 8.132 r_long_range_B_other 7.804 r_dihedral_angle_1_deg 6.691 r_scangle_other 5.689 r_scbond_it 3.82 r_scbond_other 3.82 r_mcangle_it 3.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.193 r_dihedral_angle_4_deg 19.012 r_dihedral_angle_3_deg 15.97 r_long_range_B_refined 8.132 r_long_range_B_other 7.804 r_dihedral_angle_1_deg 6.691 r_scangle_other 5.689 r_scbond_it 3.82 r_scbond_other 3.82 r_mcangle_it 3.778 r_mcangle_other 3.775 r_mcbond_it 2.729 r_mcbond_other 2.728 r_angle_refined_deg 2.032 r_angle_other_deg 0.961 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5169 Nucleic Acid Atoms Solvent Atoms 788 Heterogen Atoms 120
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling