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PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z438067480
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 28% PEG MME 2000; 0.15 M ammonium sulfate; 0.1 M sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.76 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.59 α = 90 b = 42.36 β = 90 c = 159.81 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 EIGER2 XE 9M 2021-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.918076 Diamond I04-1
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 1.61 42.36 99.4 0.069 0.075 0.03 0.998 11.9 6.3 37294
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 1.61 1.65 99 1.561 1.723 0.715 0.384 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 THROUGHOUT 1.61 40.98 35308 1939 99.11 0.20654 0.2045 0.2092 0.24291 0.2438 RANDOM 38.263
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] 0.57 -0.16 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.42 r_long_range_B_refined 9.571 r_dihedral_angle_1_deg 7.973 r_mcangle_it 4.835 r_dihedral_angle_2_deg 4.698 r_scbond_it 4.663 r_mcbond_it 3.567 r_angle_refined_deg 1.819 r_chiral_restr 0.13 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.42 r_long_range_B_refined 9.571 r_dihedral_angle_1_deg 7.973 r_mcangle_it 4.835 r_dihedral_angle_2_deg 4.698 r_scbond_it 4.663 r_mcbond_it 3.567 r_angle_refined_deg 1.819 r_chiral_restr 0.13 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2127 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction REFMAC phasing