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Crystal structure of wild-type HRP-2 PWWP domain - Crystal form P212121 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 293 2.2 M Ammonium sulfate
0.2 M Ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 3.09 60.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.883 α = 90 b = 59.833 β = 90 c = 105.778 γ = 90
Symmetry Space Group P 21 21 21
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 6M-F 2018-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97893 ESRF ID23-1
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 2.36 52.89 93 0.054 0.063 0.029 0.989 15.7 4.1 10576
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 2.36 2.49 93.9 0.33 0.387 0.193 0.66 3.9
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 2.36 52.89 9894 531 90.83 0.22084 0.21732 0.2207 0.28074 0.2872 RANDOM 53.67
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] -4.01 6.63 -2.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.587 r_long_range_B_refined 12.483 r_long_range_B_other 12.423 r_dihedral_angle_2_deg 9.901 r_dihedral_angle_1_deg 8.684 r_scangle_other 8.466 r_mcangle_other 8.044 r_mcangle_it 8.041 r_scbond_it 6.381 r_scbond_other 5.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.587 r_long_range_B_refined 12.483 r_long_range_B_other 12.423 r_dihedral_angle_2_deg 9.901 r_dihedral_angle_1_deg 8.684 r_scangle_other 8.466 r_mcangle_other 8.044 r_mcangle_it 8.041 r_scbond_it 6.381 r_scbond_other 5.573 r_mcbond_it 5.323 r_mcbond_other 5.308 r_angle_refined_deg 1.544 r_angle_other_deg 0.544 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 1385 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing