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Crystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P21212
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 293 32.5% PEG 4000
0.1 MSodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.74 55.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.332 α = 90 b = 193.363 β = 90 c = 41.93 γ = 90
Symmetry Space Group P 21 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 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 1.8 96.68 94.5 0.102 0.111 0.045 0.998 11.1 6 52808
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 1.8 1.9 93.5 1.071 1.173 0.467 0.653 5.9
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 1.8 96.68 50173 2534 94.33 0.19882 0.19732 0.2068 0.22842 0.2378 RANDOM 28.482
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] -0.23 0.64 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.738 r_dihedral_angle_1_deg 7.729 r_long_range_B_refined 7.239 r_long_range_B_other 7.188 r_dihedral_angle_2_deg 6.957 r_scangle_other 5.418 r_mcangle_it 4.09 r_mcangle_other 4.09 r_scbond_it 3.492 r_scbond_other 3.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.738 r_dihedral_angle_1_deg 7.729 r_long_range_B_refined 7.239 r_long_range_B_other 7.188 r_dihedral_angle_2_deg 6.957 r_scangle_other 5.418 r_mcangle_it 4.09 r_mcangle_other 4.09 r_scbond_it 3.492 r_scbond_other 3.49 r_mcbond_it 2.941 r_mcbond_other 2.941 r_angle_refined_deg 1.656 r_angle_other_deg 0.569 r_chiral_restr 0.086 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 3524 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing