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Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WET PDB entry 6WET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 7.5 mg/mL protein against 19-22% PEG4000, 240-270 mM trilithium/triammonium/tripotassium citrate
Crystal Properties Matthews coefficient Solvent content 3.32 62.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.01 α = 90 b = 160.143 β = 90 c = 209.632 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 PIXEL DECTRIS EIGER X 16M 2019-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953731 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.65 47.613 100 0.055 0.997 12.1 26.9 82015
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 0.816 0.508 1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 6WET 2.65 47.57 81930 4208 99.962 0.209 0.207 0.2106 0.239 0.2395 60.145
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] 1.447 3.265 -4.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.682 r_dihedral_angle_1_deg 19.328 r_dihedral_angle_4_deg 17.856 r_dihedral_angle_3_deg 15.516 r_lrange_other 10.996 r_lrange_it 10.995 r_scangle_it 6.201 r_scangle_other 6.201 r_mcangle_it 5.723 r_mcangle_other 5.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.682 r_dihedral_angle_1_deg 19.328 r_dihedral_angle_4_deg 17.856 r_dihedral_angle_3_deg 15.516 r_lrange_other 10.996 r_lrange_it 10.995 r_scangle_it 6.201 r_scangle_other 6.201 r_mcangle_it 5.723 r_mcangle_other 5.722 r_scbond_it 3.834 r_scbond_other 3.834 r_mcbond_it 3.567 r_mcbond_other 3.566 r_angle_refined_deg 1.356 r_angle_other_deg 1.185 r_metal_ion_refined 0.322 r_nbd_other 0.256 r_nbd_refined 0.197 r_symmetry_nbd_refined 0.193 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_other 0.112 r_ncsr_local_group_1 0.102 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.055 r_symmetry_xyhbond_nbd_refined 0.03 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12698 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing