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Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with L-Cysteine
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 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.38 α = 90 b = 74.38 β = 90 c = 275.49 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 2016-07-15 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 1.96 74.38 100 0.185 6.7 7.5 106771
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 1.96 2.06 0.842 2.4
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 1.96 74.38 101342 5326 99.98 0.1386 0.1383 0.1516 0.1442 0.1538 RANDOM 27.914
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 33.708 r_dihedral_angle_4_deg 17.885 r_dihedral_angle_3_deg 16.944 r_dihedral_angle_1_deg 7.469 r_angle_refined_deg 1.727 r_angle_other_deg 1.101 r_chiral_restr 0.117 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 33.708 r_dihedral_angle_4_deg 17.885 r_dihedral_angle_3_deg 16.944 r_dihedral_angle_1_deg 7.469 r_angle_refined_deg 1.727 r_angle_other_deg 1.101 r_chiral_restr 0.117 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 11624 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 104
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction