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Crystal structure of Y61AbsSHMT L-allo-Threonine external aldimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KL1 PDB ENTRY 1KL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 50% MPD, 0.1 M HEPES PH7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM L-ALLO-THREONINE
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.47 α = 90 b = 105.02 β = 90 c = 56.95 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE MARRESEARCH OSMIC MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.4 30 98.1 0.11 12.2 21.7 14402 49.6
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) 1 2.4 2.49 99.8 0.43 4.2
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 1KL1 2.41 23.1 13676 725 97.6 0.233 0.23 0.2224 0.292 0.2806 RANDOM 40.01
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] -0.02 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.618 r_dihedral_angle_3_deg 13.175 r_dihedral_angle_4_deg 9.845 r_dihedral_angle_1_deg 4.342 r_angle_refined_deg 0.881 r_scangle_it 0.455 r_nbtor_refined 0.29 r_scbond_it 0.262 r_mcangle_it 0.247 r_nbd_refined 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.618 r_dihedral_angle_3_deg 13.175 r_dihedral_angle_4_deg 9.845 r_dihedral_angle_1_deg 4.342 r_angle_refined_deg 0.881 r_scangle_it 0.455 r_nbtor_refined 0.29 r_scbond_it 0.262 r_mcangle_it 0.247 r_nbd_refined 0.156 r_mcbond_it 0.138 r_symmetry_vdw_refined 0.118 r_symmetry_hbond_refined 0.094 r_xyhbond_nbd_refined 0.082 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_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 3109 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing