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Structure of Cerezyme at pH 4.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 1.1 M (NH4)2SO4, 0.19 M guanidine HCl, 0.04 M KCl, 0.1 M Na acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.25 62.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.07 α = 90 b = 285.865 β = 90 c = 91.936 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 16M 2018-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.59 142.93 100 0.147 0.055 0.998 7.2 7.9 1531796 193710
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.62 6.202 2.348 0.676 0.5 7.9 74996
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 2NT0 1.59 77.442 193668 9698 99.956 0.216 0.2146 0.2374 0.2448 0.2686 32.082
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] 4.921 -1.64 -3.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.178 r_dihedral_angle_other_1_deg 35.453 r_dihedral_angle_4_deg 16.146 r_dihedral_angle_3_deg 14.737 r_dihedral_angle_1_deg 7.578 r_lrange_it 7.361 r_lrange_other 7.345 r_scangle_it 5.438 r_scangle_other 5.438 r_scbond_it 3.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.178 r_dihedral_angle_other_1_deg 35.453 r_dihedral_angle_4_deg 16.146 r_dihedral_angle_3_deg 14.737 r_dihedral_angle_1_deg 7.578 r_lrange_it 7.361 r_lrange_other 7.345 r_scangle_it 5.438 r_scangle_other 5.438 r_scbond_it 3.547 r_scbond_other 3.546 r_mcangle_other 3.439 r_mcangle_it 3.435 r_mcbond_it 2.514 r_mcbond_other 2.464 r_angle_refined_deg 1.587 r_angle_other_deg 1.36 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.192 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.176 r_nbd_other 0.17 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.166 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.082 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7833 Nucleic Acid Atoms Solvent Atoms 715 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing