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Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG 3350, Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.03 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.42 α = 90 b = 66.719 β = 116.25 c = 134.961 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M Rh coated collimating mirrors, K-B focusing mirrors 2017-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.18076 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.9 121.042 95 0.132 0.16 0.089 3.7 2.9 155855 155855
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 89.1 0.596 0.596 0.725 0.407 1.1 2.6
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 2GSU 1.9 30.04 147590 7565 94.48 0.2458 0.2429 0.2488 0.303 0.3049 RANDOM 37.325
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] -3.83 0.24 1.26 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.552 r_dihedral_angle_4_deg 15.37 r_dihedral_angle_3_deg 15.039 r_dihedral_angle_1_deg 7.134 r_angle_refined_deg 1.679 r_angle_other_deg 1.182 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.552 r_dihedral_angle_4_deg 15.37 r_dihedral_angle_3_deg 15.039 r_dihedral_angle_1_deg 7.134 r_angle_refined_deg 1.679 r_angle_other_deg 1.182 r_chiral_restr 0.097 r_bond_refined_d 0.013 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 17587 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction