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Crystal structure of E53QbsSHMT obtained in the presence of glycine and 5-fomyl tetrahydrofolate
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 7.5 50% MPD, 0.1 M HEPES PH 7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM GLYCINE PROTEIN INCUBATED WITH 2 MM 5-FORMYL TETRAHYDROFOLATE
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.964 α = 90 b = 106.46 β = 90 c = 56.99 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 1.86 50 98.8 0.05 17.5 4.2 346889 25
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 1.86 1.93 92 0.38 3.2 3.5
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1KL1 1.86 27.01 27207 3029 95.2 0.172 0.168 0.1665 0.207 0.2062 RANDOM 21.02
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.859 r_dihedral_angle_4_deg 15.676 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 5.491 r_scangle_it 2.903 r_scbond_it 1.906 r_angle_refined_deg 1.298 r_mcangle_it 1.008 r_mcbond_it 0.644 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.859 r_dihedral_angle_4_deg 15.676 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 5.491 r_scangle_it 2.903 r_scbond_it 1.906 r_angle_refined_deg 1.298 r_mcangle_it 1.008 r_mcbond_it 0.644 r_nbtor_refined 0.296 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.191 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 3117 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling