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Crystal Structure of a Novel-type Phosphoserine Phosphatase from <i>Hydrogenobacter thermophilus</i> TK-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100mM HEPES-NaOH, 10%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.81 α = 90 b = 73.63 β = 90 c = 124.28 γ = 90
Symmetry Space Group P 21 21 21
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 MAR225HE 2011-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 36.1 8.6 73684 73612
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 1H2E 1.5 36.1 73608 3714 99.88 0.1843 0.1836 0.1927 0.1966 0.2081 RANDOM 16.45
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] 0.22 -0.06 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.824 r_dihedral_angle_4_deg 15.717 r_dihedral_angle_3_deg 11.974 r_dihedral_angle_1_deg 5.932 r_angle_refined_deg 1.272 r_angle_other_deg 0.772 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.824 r_dihedral_angle_4_deg 15.717 r_dihedral_angle_3_deg 11.974 r_dihedral_angle_1_deg 5.932 r_angle_refined_deg 1.272 r_angle_other_deg 0.772 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3456 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction XDS data scaling