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Crystal structure of Ser33 in complex with L-Serine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M sodium citrate tribasic
0.1 M Bis-Tris propane pH 8.5
20% w/v PEG 3350
7.4 mg/ml of protein in 25 mM Tris pH=7.5 and 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.115 α = 64.42 b = 110.735 β = 65.95 c = 117.027 γ = 67.03
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 DECTRIS PILATUS3 6M 2020-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.69 43.11 96.97 0.988 9.57 4.3 114590
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.691 2.787 0.893 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.69 43.11 1.96 114028 5996 96.99 0.2184 0.2157 0.2168 0.2645 0.2644
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 f_dihedral_angle_d 10.877 f_angle_d 1.031 f_chiral_restr 0.057 f_bond_d 0.013 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25922 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing