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Crystal structures of human E-NPP 1: apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B56 PDB entry 4B56
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 3.3 62.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.111 α = 90 b = 158.885 β = 90 c = 209.832 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 2019-08-03 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 2.6 44.423 100 0.053 0.998 12.9 26.1 86202
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 2.6 2.65 100 0.916 0.539 1 14.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4B56 2.6 44.4 86169 4461 99.962 0.212 0.2104 0.2442 0.215 68.659
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] 2.237 2.855 -5.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_1_deg 19.331 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_3_deg 16.057 r_lrange_it 11.668 r_lrange_other 11.668 r_scangle_it 7.136 r_scangle_other 7.136 r_mcangle_it 6.615 r_mcangle_other 6.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_1_deg 19.331 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_3_deg 16.057 r_lrange_it 11.668 r_lrange_other 11.668 r_scangle_it 7.136 r_scangle_other 7.136 r_mcangle_it 6.615 r_mcangle_other 6.614 r_scbond_it 4.525 r_scbond_other 4.524 r_mcbond_it 4.254 r_mcbond_other 4.254 r_angle_refined_deg 1.37 r_angle_other_deg 1.192 r_symmetry_nbd_refined 0.269 r_nbd_other 0.268 r_symmetry_xyhbond_nbd_refined 0.243 r_metal_ion_refined 0.218 r_nbd_refined 0.204 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_other 0.125 r_ncsr_local_group_1 0.105 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12653 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 237
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing