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Crystal structure of CbiL in complex with S-adenosylhomocysteine, a methyltransferase involved in anaerobic vitamin B12 biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E0K PDB ENTRY 2E0K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 15% PEG 3350, 0.2M ammonium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.822 α = 90 b = 87.822 β = 90 c = 123.562 γ = 90
Symmetry Space Group P 43 21 2
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 315 2005-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 99.6 0.071 11 11.2 33275 33275
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 96.8 0.327 5.7
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 PDB ENTRY 2E0K 2 50 31513 1679 99.56 0.2248 0.22263 0.2183 0.26598 0.2617 RANDOM 31.825
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] -0.38 -0.38 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.476 r_dihedral_angle_4_deg 19.687 r_dihedral_angle_3_deg 18.473 r_dihedral_angle_1_deg 8.303 r_scangle_it 3.126 r_scbond_it 2.125 r_angle_refined_deg 1.978 r_mcangle_it 1.499 r_mcbond_it 0.984 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.476 r_dihedral_angle_4_deg 19.687 r_dihedral_angle_3_deg 18.473 r_dihedral_angle_1_deg 8.303 r_scangle_it 3.126 r_scbond_it 2.125 r_angle_refined_deg 1.978 r_mcangle_it 1.499 r_mcbond_it 0.984 r_nbtor_refined 0.309 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.241 r_symmetry_hbond_refined 0.238 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.152 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 3452 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing