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Crystal structure of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 0.2 M KCl, 0.1 M MgAcetate, 0.05 NaCacodylate pH 6.0, 10.2% PEG8000, 1 mM CaCl2, 0.1 mM ZnSO4
Crystal Properties Matthews coefficient Solvent content 2.95 58.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.843 α = 90 b = 124.063 β = 97.03 c = 110.673 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 2015-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91843 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.4 47.35 99.5 0.131 7.6 3.4 76975 63.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.45
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 2XR9 2.4 47.35 76975 1539 99.5 0.215 0.215 0.229 0.2381 RANDOM 57.83
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] -0.148 1.9452 -10.6403 10.7883
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.87 t_omega_torsion 2.22 t_angle_deg 0.95 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.87 t_omega_torsion 2.22 t_angle_deg 0.95 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11524 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 234
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling BUSTER phasing