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Crystal structure of F351GbsSHMT in complex with Gly and FTHF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KL2 PDB ENTRY 1KL2
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 GLY, PROTEIN INCUBATED WITH 2 MM FTHF
Crystal Properties Matthews coefficient Solvent content 2.06 39.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.382 α = 90 b = 103.483 β = 90.33 c = 61.959 γ = 90
Symmetry Space Group P 1 21 1
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 2.7 30 98.7 0.09 10 3.5 19879 77.4
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 2.7 2.8 99.8 0.51 2.4 3.4
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 1KL2 2.7 20.81 18654 1007 98.7 0.218 0.215 0.2148 0.263 0.2679 RANDOM 57.76
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 -0.06 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.291 r_dihedral_angle_3_deg 15.453 r_dihedral_angle_4_deg 13.051 r_dihedral_angle_1_deg 4.669 r_angle_refined_deg 0.985 r_scangle_it 0.679 r_scbond_it 0.394 r_mcangle_it 0.356 r_nbtor_refined 0.294 r_mcbond_it 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.291 r_dihedral_angle_3_deg 15.453 r_dihedral_angle_4_deg 13.051 r_dihedral_angle_1_deg 4.669 r_angle_refined_deg 0.985 r_scangle_it 0.679 r_scbond_it 0.394 r_mcangle_it 0.356 r_nbtor_refined 0.294 r_mcbond_it 0.197 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.061 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 6218 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing