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Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with O-Phosphoserine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 0.1M sodium N-2-hydroxyethylpiperazine-N'-2-ethanesulfonate buffer, pH 8.2 (7.9), 29%(v/v) 2-propanol, 13% (11%) (v/v) polyethylene glycol 4,000, and 11mM TCEP-HCl
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.2 α = 90 b = 75.2 β = 90 c = 275.28 γ = 90
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 Bruker DIP-6040 2013-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.58 75.2 100 0.133 7.5 7.5 208050
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 1.58 1.66 1.038 1.7
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 5B3A 1.58 75.2 197722 10205 99.96 0.1669 0.1665 0.175 0.1744 0.1804 RANDOM 24.685
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 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.673 r_dihedral_angle_4_deg 17.477 r_dihedral_angle_3_deg 15.574 r_dihedral_angle_1_deg 7.086 r_angle_refined_deg 1.763 r_angle_other_deg 1.06 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.673 r_dihedral_angle_4_deg 17.477 r_dihedral_angle_3_deg 15.574 r_dihedral_angle_1_deg 7.086 r_angle_refined_deg 1.763 r_angle_other_deg 1.06 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11648 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 120
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction