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Crystal structure of E53QbsSHMT internal aldimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KKJ PDB ENTRY 1KKJ
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
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.07 α = 90 b = 106.733 β = 90 c = 56.884 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 50 99.1 0.07 14.9 3.3 25550 25.3
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 2.07 99.4 0.4 2.7 3.2
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1KKJ 2 29.36 23004 2509 98.9 0.179 0.175 0.1756 0.218 0.2169 RANDOM 22.45
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] 0.03 -0.05 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.399 r_dihedral_angle_4_deg 19.009 r_dihedral_angle_3_deg 14.052 r_dihedral_angle_1_deg 5.577 r_scangle_it 2.326 r_scbond_it 1.476 r_angle_refined_deg 1.217 r_mcangle_it 0.824 r_mcbond_it 0.499 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.399 r_dihedral_angle_4_deg 19.009 r_dihedral_angle_3_deg 14.052 r_dihedral_angle_1_deg 5.577 r_scangle_it 2.326 r_scbond_it 1.476 r_angle_refined_deg 1.217 r_mcangle_it 0.824 r_mcbond_it 0.499 r_nbtor_refined 0.297 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.163 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 249 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling