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X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with aptamer A9g
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.2 Mg Acet, 40% (v/v) MPD, 1 mM 2-PMPA
Crystal Properties Matthews coefficient Solvent content 4.25 71.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.096 α = 90 b = 121.096 β = 90 c = 216.271 γ = 90
Symmetry Space Group P 41 21 2
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 2017-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.2 105.66 100 0.164 0.172 0.048 0.838 10.1 12.6 82266 36.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 100 0.985 1.026 0.284 0.578 2 12.9
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-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 FREE R-VALUE 2OOT 2.2 105.66 82168 4036 99.989 0.195 0.195 0.192 0.2021 0.217 0.2068 Random 44
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] 1.711 1.711 -3.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.279 r_dihedral_angle_3_deg 15.204 r_dihedral_angle_4_deg 14.367 r_dihedral_angle_1_deg 6.937 r_lrange_it 6.168 r_lrange_other 6.151 r_scangle_it 4.632 r_scangle_other 4.631 r_mcangle_it 3.496 r_mcangle_other 3.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.279 r_dihedral_angle_3_deg 15.204 r_dihedral_angle_4_deg 14.367 r_dihedral_angle_1_deg 6.937 r_lrange_it 6.168 r_lrange_other 6.151 r_scangle_it 4.632 r_scangle_other 4.631 r_mcangle_it 3.496 r_mcangle_other 3.496 r_scbond_it 3.062 r_scbond_other 3.062 r_mcbond_it 2.344 r_mcbond_other 2.344 r_angle_refined_deg 1.636 r_angle_other_deg 1.374 r_nbd_other 0.209 r_symmetry_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.192 r_nbd_refined 0.18 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.162 r_symmetry_nbd_refined 0.145 r_symmetry_nbtor_other 0.108 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.007 r_bond_other_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5521 Nucleic Acid Atoms 907 Solvent Atoms 401 Heterogen Atoms 321
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing