☰ Navigation Tabs
Crystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P21 type 3
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 2.5 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.24 44.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.2 α = 90 b = 41.172 β = 100.37 c = 70.567 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 PILATUS 6M-F 2020-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 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 1.93 69.41 96.4 0.087 0.107 0.062 0.996 7.4 2.7 20685
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 1.93 2.04 98.1 0.918 1.129 0.647 0.755 2.8
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 1.93 69.41 19654 1015 96.04 0.24589 0.24271 0.2475 0.30952 0.3062 RANDOM 31.083
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] -1.02 -3.66 -0.78 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.938 r_dihedral_angle_2_deg 9.825 r_dihedral_angle_1_deg 8.462 r_long_range_B_refined 7.439 r_long_range_B_other 7.42 r_scangle_other 5.036 r_mcangle_it 4.737 r_mcangle_other 4.735 r_scbond_it 3.373 r_scbond_other 3.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.938 r_dihedral_angle_2_deg 9.825 r_dihedral_angle_1_deg 8.462 r_long_range_B_refined 7.439 r_long_range_B_other 7.42 r_scangle_other 5.036 r_mcangle_it 4.737 r_mcangle_other 4.735 r_scbond_it 3.373 r_scbond_other 3.175 r_mcbond_it 3.082 r_mcbond_other 3.068 r_angle_refined_deg 1.617 r_angle_other_deg 0.581 r_chiral_restr 0.085 r_gen_planes_refined 0.008 r_bond_refined_d 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 2055 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing