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Crystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P1 type 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.2 M Ammonium acetate
32.5% PEG 4000
0.1 M Trisodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.21 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.959 α = 63.11 b = 37.866 β = 70.26 c = 41.818 γ = 74.37
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 9M 2020-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.99988 SOLEIL PROXIMA 2
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 1.58 36.1 90.1 0.081 0.102 0.06 0.99 5.4 2.4 22743
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 1.58 1.66 94.9 0.594 0.75 0.451 0.667 2.6
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 1.58 36.1 21540 1168 89.99 0.18044 0.17848 0.1883 0.21631 0.2226 RANDOM 19.337
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] -0.27 -0.23 0.77 0.46 0.37 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.433 r_dihedral_angle_1_deg 8.026 r_long_range_B_refined 6.466 r_long_range_B_other 6.262 r_scangle_other 4.283 r_mcangle_other 3.52 r_mcangle_it 3.51 r_dihedral_angle_2_deg 2.91 r_scbond_it 2.737 r_scbond_other 2.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.433 r_dihedral_angle_1_deg 8.026 r_long_range_B_refined 6.466 r_long_range_B_other 6.262 r_scangle_other 4.283 r_mcangle_other 3.52 r_mcangle_it 3.51 r_dihedral_angle_2_deg 2.91 r_scbond_it 2.737 r_scbond_other 2.736 r_mcbond_it 2.26 r_mcbond_other 2.258 r_angle_refined_deg 1.568 r_angle_other_deg 0.555 r_chiral_restr 0.081 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1445 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing