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Crystal structure of Y60AbsSHMT 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 = 61.334 α = 90 b = 106.674 β = 90 c = 57.124 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 1.7 30 95.9 0.04 37.4 5.2 40505 21.6
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 1.7 1.76 93.1 0.21 7.9 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 1KKJ 1.7 22.48 38264 2034 95.9 0.183 0.182 0.1784 0.208 0.2058 RANDOM 16.67
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.105 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 13.096 r_dihedral_angle_1_deg 5.233 r_scangle_it 1.928 r_scbond_it 1.202 r_angle_refined_deg 1.074 r_mcangle_it 0.65 r_mcbond_it 0.409 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.105 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 13.096 r_dihedral_angle_1_deg 5.233 r_scangle_it 1.928 r_scbond_it 1.202 r_angle_refined_deg 1.074 r_mcangle_it 0.65 r_mcbond_it 0.409 r_nbtor_refined 0.3 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.164 r_symmetry_hbond_refined 0.102 r_xyhbond_nbd_refined 0.095 r_chiral_restr 0.073 r_bond_refined_d 0.007 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 3109 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing