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Serine Hydroxymethyltransferase Y55F Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 0.1M Hepes (N-(2-hydroxylethyl)piperazine-N -2 ethansulfonic acid) pH 7.5, 1.4M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.41 48.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.59 α = 90 b = 112.59 β = 90 c = 68.929 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 CCD MARMOSAIC 225 mm CCD 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.97623 BESSY 14.1
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 3.3 50 94 0.13 9.7 4.3 6600
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 3.3 3.42 97.3 0.48 2.5 4.3 734
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 1dfo 3.3 50 6356 319 94.76 0.25625 0.25528 0.2929 0.27535 0.2869 RANDOM 39.946
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] 3.17 3.17 -6.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.637 r_dihedral_angle_3_deg 14.009 r_dihedral_angle_4_deg 3.504 r_dihedral_angle_1_deg 3.404 r_angle_refined_deg 0.776 r_nbtor_refined 0.284 r_nbd_refined 0.134 r_symmetry_vdw_refined 0.095 r_scangle_it 0.089 r_xyhbond_nbd_refined 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.637 r_dihedral_angle_3_deg 14.009 r_dihedral_angle_4_deg 3.504 r_dihedral_angle_1_deg 3.404 r_angle_refined_deg 0.776 r_nbtor_refined 0.284 r_nbd_refined 0.134 r_symmetry_vdw_refined 0.095 r_scangle_it 0.089 r_xyhbond_nbd_refined 0.066 r_scbond_it 0.051 r_chiral_restr 0.05 r_mcangle_it 0.04 r_symmetry_hbond_refined 0.031 r_mcbond_it 0.022 r_bond_refined_d 0.005 r_gen_planes_refined 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3185 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement