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Crystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P1 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 5 277 0.4 M ammonium acetate pH 5.0
30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.127 α = 62.08 b = 42.59 β = 76.38 c = 44.242 γ = 87
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 0.9999 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 1.05 36.66 88.6 0.062 0.067 0.025 0.999 14.4 6.8 85077
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 1.05 1.11 66.5 1.257 1.388 0.573 0.672 5.3
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 1.05 36.65 80135 4232 87.84 0.16515 0.16394 0.1634 0.18808 0.1874 RANDOM 13.452
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] -0.05 -0.22 0.04 -0.06 0.07 0.1
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 21.237 r_long_range_B_other 18.61 r_dihedral_angle_3_deg 11.024 r_scangle_other 8.597 r_dihedral_angle_1_deg 7.967 r_mcangle_other 7.275 r_mcangle_it 7.273 r_scbond_it 6.034 r_scbond_other 6.03 r_mcbond_it 5.079
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 21.237 r_long_range_B_other 18.61 r_dihedral_angle_3_deg 11.024 r_scangle_other 8.597 r_dihedral_angle_1_deg 7.967 r_mcangle_other 7.275 r_mcangle_it 7.273 r_scbond_it 6.034 r_scbond_other 6.03 r_mcbond_it 5.079 r_mcbond_other 5.057 r_rigid_bond_restr 4.32 r_dihedral_angle_2_deg 3.399 r_angle_refined_deg 1.821 r_angle_other_deg 0.631 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1482 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing