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Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 ammonium sulfate, HEPES, PEG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.628 α = 90 b = 88.095 β = 101.78 c = 88.764 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 SBC-3 mirrors 2004-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9793 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.08 41.2 0.114 6.8 6.7 42879 41510
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.08 2.18 81.7 0.432 2.4 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 SAD THROUGHOUT 2.08 41.2 37355 37355 4121 95.97 0.21916 0.21165 0.2108 0.28797 0.287 RANDOM 31.376
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] -2.29 0.15 -1.99 4.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.355 r_dihedral_angle_3_deg 19.061 r_dihedral_angle_4_deg 18.849 r_dihedral_angle_1_deg 6.276 r_scangle_it 1.852 r_angle_refined_deg 1.447 r_scbond_it 1.195 r_mcangle_it 0.856 r_mcbond_it 0.505 r_nbd_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.355 r_dihedral_angle_3_deg 19.061 r_dihedral_angle_4_deg 18.849 r_dihedral_angle_1_deg 6.276 r_scangle_it 1.852 r_angle_refined_deg 1.447 r_scbond_it 1.195 r_mcangle_it 0.856 r_mcbond_it 0.505 r_nbd_refined 0.333 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.152 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 5954 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling SHARP phasing