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Crystal structure of L-Serine Hydroxymethyltransferase in complex with a mixture of L-Threonine and Glycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WXB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 HEPES 20 mM pH 7.5,
Sodium citrate 1.1 M,
Cacodylate 0.1 M pH 6,5
Crystal Properties Matthews coefficient Solvent content 3.43 64.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.43 α = 90 b = 115.43 β = 90 c = 191.48 γ = 90
Symmetry Space Group P 41 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 PIXEL PSI PILATUS 6M 2009-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.000 ESRF ID29
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 99 99.9 0.088 14.4 8.1 82377
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 2.1 96.8 0.672 2.2 8
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 4WXB 2 49.43 82377 4344 98.6 0.172 0.171 0.1811 0.203 0.2094 RANDOM 36.8
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.094 r_dihedral_angle_4_deg 18.806 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 2.014 r_angle_other_deg 0.936 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.094 r_dihedral_angle_4_deg 18.806 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 2.014 r_angle_other_deg 0.936 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6248 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing