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The crystal structure of Bacillus subtilis YtqB in complex with SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PON
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 30-36% PEG200/5% PEG2000/0.1M sodium cacodylate (pH 6.5) or 30-36% PEG200/5% PEG2000/0.1 M Hepes (pH 7.0) , VAPOR DIFFUSION, SITTING DROP, temperature 291 K
Crystal Properties Matthews coefficient Solvent content 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.066 α = 90 b = 77.661 β = 90 c = 100.481 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 270 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) PAL/PLS 7A (6B, 6C1)
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 30 99.6 19185
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 2.28 98.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4PON 2.2 30 18155 982 99.43 0.22207 0.22013 0.2171 0.25995 0.2542 RANDOM 52.166
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] -0.67 0.41 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.97 r_dihedral_angle_3_deg 16.699 r_dihedral_angle_4_deg 12.417 r_dihedral_angle_1_deg 6.526 r_scangle_it 3.504 r_scbond_it 2.215 r_angle_refined_deg 1.588 r_mcangle_it 1.239 r_angle_other_deg 0.977 r_mcbond_it 0.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.97 r_dihedral_angle_3_deg 16.699 r_dihedral_angle_4_deg 12.417 r_dihedral_angle_1_deg 6.526 r_scangle_it 3.504 r_scbond_it 2.215 r_angle_refined_deg 1.588 r_mcangle_it 1.239 r_angle_other_deg 0.977 r_mcbond_it 0.701 r_mcbond_other 0.198 r_chiral_restr 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2595 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling