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Crystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P21 type 1
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
27% PEG 4000
0.1 M Sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.79 55.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.686 α = 90 b = 80.923 β = 102.34 c = 108.723 γ = 90
Symmetry Space Group P 1 21 1
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 0.98011 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 2.08 53.11 100 0.172 0.186 0.07 0.993 7.4 7 42492
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 2.08 2.19 100 1.753 1.893 0.708 0.639 7.1
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 2.08 53.1 40160 2132 99.56 0.2013 0.19858 0.2055 0.25431 0.257 RANDOM 34.779
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] 0.31 -0.28 1.88 -1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.852 r_long_range_B_refined 8.571 r_long_range_B_other 8.562 r_dihedral_angle_1_deg 8.36 r_dihedral_angle_2_deg 7.575 r_scangle_other 6.609 r_mcangle_it 5.576 r_mcangle_other 5.576 r_scbond_it 4.322 r_scbond_other 4.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.852 r_long_range_B_refined 8.571 r_long_range_B_other 8.562 r_dihedral_angle_1_deg 8.36 r_dihedral_angle_2_deg 7.575 r_scangle_other 6.609 r_mcangle_it 5.576 r_mcangle_other 5.576 r_scbond_it 4.322 r_scbond_other 4.322 r_mcbond_it 3.749 r_mcbond_other 3.744 r_angle_refined_deg 1.824 r_angle_other_deg 0.62 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 4271 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing