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Complex structure of PHF19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 2.3M ammonium phosphate dibasic and 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.477 α = 90 b = 111.477 β = 90 c = 34.409 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2016-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97951 CLSI 08B1-1
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 1.71 55.74 99.4 0.048 0.054 0.023 1 21.6 5.4 51838
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 1.71 1.74 92.1 1.314 1.608 0.906 0.19 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4HCZ 1.75 48.271 48195 2242 99.921 0.215 0.213 0.1962 0.2497 0.2407 26.856
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] 3.308 3.308 -6.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.667 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 15.721 r_dihedral_angle_1_deg 8.526 r_lrange_other 5.611 r_lrange_it 5.61 r_scangle_it 4.463 r_scangle_other 4.463 r_mcangle_it 4.131 r_mcangle_other 4.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.667 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 15.721 r_dihedral_angle_1_deg 8.526 r_lrange_other 5.611 r_lrange_it 5.61 r_scangle_it 4.463 r_scangle_other 4.463 r_mcangle_it 4.131 r_mcangle_other 4.13 r_scbond_it 3.384 r_scbond_other 3.383 r_mcbond_it 3.216 r_mcbond_other 3.216 r_angle_refined_deg 1.994 r_angle_other_deg 1.289 r_nbd_other 0.202 r_symmetry_nbd_refined 0.195 r_nbd_refined 0.193 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.133 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3031 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 11
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing