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Crystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form C2
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 4.6 293 0.15 M Ammonium sulfate
28% PEG MME 2000
0.1 M Sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.7 54.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.086 α = 90 b = 41.835 β = 102.21 c = 72.257 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 2M 2021-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99999 SLS X06DA
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 1.41 38.19 91.3 0.146 0.159 0.063 0.996 11.3 6.2 40436
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 1.41 1.49 83.8 2.083 2.284 0.919 0.499 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 1.41 38.19 37913 1939 89.96 0.18187 0.1805 0.1802 0.20841 0.208 RANDOM 12.26
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] 0.39 0.38 -0.41 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.461 r_long_range_B_refined 7.772 r_long_range_B_other 7.437 r_dihedral_angle_1_deg 7.373 r_dihedral_angle_2_deg 7.013 r_scangle_other 4.062 r_mcangle_other 2.806 r_mcangle_it 2.799 r_scbond_it 2.747 r_scbond_other 2.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.461 r_long_range_B_refined 7.772 r_long_range_B_other 7.437 r_dihedral_angle_1_deg 7.373 r_dihedral_angle_2_deg 7.013 r_scangle_other 4.062 r_mcangle_other 2.806 r_mcangle_it 2.799 r_scbond_it 2.747 r_scbond_other 2.55 r_angle_refined_deg 1.78 r_mcbond_it 1.732 r_mcbond_other 1.731 r_angle_other_deg 0.637 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 1452 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing