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Crystal structure of bifunctional methyltransferase YcbY (RlmLK) from Escherichia coli, SAH binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B78 2B78, 3LDG, 3LDF experimental model PDB 3LDG 2B78, 3LDG, 3LDF experimental model PDB 3LDF 2B78, 3LDG, 3LDF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.1M HEPES, 12%(w/v) PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.3 62.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.646 α = 90 b = 140.834 β = 102.3 c = 102.866 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD 2010-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U SSRF BL17U
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 2.2 50 96.8 99787 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 96.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2B78, 3LDG, 3LDF 2.2 49.91 94748 4970 96.13 0.18877 0.18638 0.23392 0.2535 RANDOM 51.91
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] 1.21 -3.18 -2.65 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.467 r_dihedral_angle_3_deg 20.714 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_1_deg 7.137 r_scangle_it 5.055 r_scbond_it 3.298 r_angle_refined_deg 2.191 r_mcangle_it 2.025 r_mcbond_it 1.125 r_chiral_restr 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.467 r_dihedral_angle_3_deg 20.714 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_1_deg 7.137 r_scangle_it 5.055 r_scbond_it 3.298 r_angle_refined_deg 2.191 r_mcangle_it 2.025 r_mcbond_it 1.125 r_chiral_restr 0.191 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10037 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 189
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling