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Crystal structure of methylornithine synthase (PylB)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100 mM Tris-hydrochloride, 200 mM MgCl2, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.02 α = 90 b = 77.02 β = 90 c = 104.95 γ = 120
Symmetry Space Group P 32 2 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 PIXEL PSI PILATUS 6M 2011-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 20 99.8 0.071 0.079 12.6 5.4 58172 58074 2.5 2.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.6 99.9 0.539 0.525 3.2 5.3
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 MOLECULAR REPLACEMENT THROUGHOUT 1.5 10 57839 55170 2904 99.83 0.13049 0.12865 0.1304 0.16504 0.1657 RANDOM 25.247
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.259 r_dihedral_angle_2_deg 35.165 r_dihedral_angle_4_deg 15.308 r_sphericity_bonded 14.847 r_dihedral_angle_3_deg 12.872 r_rigid_bond_restr 8.312 r_dihedral_angle_1_deg 5.96 r_scangle_it 4.963 r_scbond_it 3.188 r_angle_refined_deg 2.576
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.259 r_dihedral_angle_2_deg 35.165 r_dihedral_angle_4_deg 15.308 r_sphericity_bonded 14.847 r_dihedral_angle_3_deg 12.872 r_rigid_bond_restr 8.312 r_dihedral_angle_1_deg 5.96 r_scangle_it 4.963 r_scbond_it 3.188 r_angle_refined_deg 2.576 r_mcangle_it 2.529 r_mcbond_it 1.418 r_chiral_restr 0.289 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2699 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 45
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing