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Crystal structure of Y60AbsSHMT crystallized in the presence of L- allo-Thr
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 L-ALLO-THR
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.281 α = 90 b = 106.571 β = 90 c = 57.19 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 1.84 30 93.2 0.08 13.1 6 30945 25.7
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 1.84 1.91 97.2 0.46 3.2 5.4
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 1.84 22.28 29357 1542 92.9 0.196 0.195 0.194 0.227 0.2247 RANDOM 24.55
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 0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.004 r_dihedral_angle_4_deg 15.946 r_dihedral_angle_3_deg 13.391 r_dihedral_angle_1_deg 5.43 r_scangle_it 2.143 r_scbond_it 1.331 r_angle_refined_deg 1.18 r_mcangle_it 0.739 r_mcbond_it 0.464 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.004 r_dihedral_angle_4_deg 15.946 r_dihedral_angle_3_deg 13.391 r_dihedral_angle_1_deg 5.43 r_scangle_it 2.143 r_scbond_it 1.331 r_angle_refined_deg 1.18 r_mcangle_it 0.739 r_mcbond_it 0.464 r_nbtor_refined 0.297 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.163 r_symmetry_hbond_refined 0.119 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.078 r_bond_refined_d 0.009 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 3107 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing