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Crystal structure of truncated Acylphosphatase from S. sulfataricus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 2.0 M NaCl, 10% PEG 6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.67 26.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.15 α = 90 b = 41.33 β = 90 c = 91.4 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 110 CCD MAR CCD 165 mm bent collimating mirror and toroid 2013-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.0716 ESRF BM14
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 1.7 24.58 97.1 0.129 11.4 5.3 17814 17297 14
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 1.7 1.79 91.2 0.404 4.4 5.3 2328
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4OIX 1.7 24.58 16390 861 95.9 0.16939 0.16682 0.21968 0.2292 RANDOM 12.483
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] -9.76 -10.8 20.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.457 r_sphericity_free 18.039 r_dihedral_angle_4_deg 17.994 r_dihedral_angle_3_deg 15.666 r_dihedral_angle_1_deg 6.024 r_sphericity_bonded 4.858 r_rigid_bond_restr 4.829 r_angle_refined_deg 1.422 r_angle_other_deg 1.086 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.457 r_sphericity_free 18.039 r_dihedral_angle_4_deg 17.994 r_dihedral_angle_3_deg 15.666 r_dihedral_angle_1_deg 6.024 r_sphericity_bonded 4.858 r_rigid_bond_restr 4.829 r_angle_refined_deg 1.422 r_angle_other_deg 1.086 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1450 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 5
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling