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Crystal structure of Y61AbsSHMT L-Serine external aldimine
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 50% MPD, 0.1 M HEPES PH7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM L-SERINE
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.35 α = 90 b = 105.23 β = 90 c = 56.93 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 MIRRORS 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 2.4 30 93.6 0.08 18.6 33 13694 47.3
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 2.4 2.49 99.2 0.42 4.5
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1KL1 2.42 23.88 13006 679 93.3 0.242 0.24 0.232 0.292 0.2816 RANDOM 41.75
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] 0.05 0.08 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.28 r_dihedral_angle_3_deg 13.505 r_dihedral_angle_4_deg 11.268 r_dihedral_angle_1_deg 4.346 r_angle_refined_deg 0.873 r_scangle_it 0.419 r_nbtor_refined 0.29 r_mcangle_it 0.251 r_scbond_it 0.244 r_nbd_refined 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.28 r_dihedral_angle_3_deg 13.505 r_dihedral_angle_4_deg 11.268 r_dihedral_angle_1_deg 4.346 r_angle_refined_deg 0.873 r_scangle_it 0.419 r_nbtor_refined 0.29 r_mcangle_it 0.251 r_scbond_it 0.244 r_nbd_refined 0.155 r_mcbond_it 0.139 r_symmetry_vdw_refined 0.124 r_xyhbond_nbd_refined 0.094 r_symmetry_hbond_refined 0.09 r_chiral_restr 0.055 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 3109 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing