☰ Navigation Tabs
Crystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P21 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, SITTING DROP 8.5 277 0.2 M Ammonium dihydrogen phosphate
50% MPD
0.1 M TRIS pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.74 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.109 α = 90 b = 70.989 β = 118.26 c = 44.458 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 1.54 37.09 90.6 0.134 0.164 0.093 0.984 3.3 2.6 30555
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 1.54 1.63 85.3 1.108 1.417 0.87 0.582 2.2
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 1.54 37.09 29005 1487 89.66 0.18953 0.18764 0.1941 0.2269 0.2288 RANDOM 18.752
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] -9.39 -0.92 18.49 -9.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.907 r_dihedral_angle_1_deg 8.18 r_long_range_B_refined 4.949 r_long_range_B_other 4.942 r_dihedral_angle_2_deg 4.41 r_scangle_other 3.943 r_mcangle_it 3.373 r_mcangle_other 3.371 r_scbond_it 2.894 r_scbond_other 2.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.907 r_dihedral_angle_1_deg 8.18 r_long_range_B_refined 4.949 r_long_range_B_other 4.942 r_dihedral_angle_2_deg 4.41 r_scangle_other 3.943 r_mcangle_it 3.373 r_mcangle_other 3.371 r_scbond_it 2.894 r_scbond_other 2.893 r_mcbond_it 2.542 r_mcbond_other 2.542 r_angle_refined_deg 2.288 r_angle_other_deg 0.851 r_chiral_restr 0.133 r_gen_planes_refined 0.015 r_bond_refined_d 0.013 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 1446 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing