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Crystal structure of PWWP-DNA complex for human hepatoma-derived growth factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XSL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Sodium nitrate, Sodium phosphate dibasic, Ammonium sulfate, Tris, Bicine, MPD, PEG 1000, PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.73 33.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.402 α = 90 b = 32.402 β = 90 c = 205.82 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 110 CCD RAYONIX MX300-HS 2016-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.84 30 98.7 0.109 0.135 17.25 8.3 5853
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.94 90.6 0.585 0.507 2.57 3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XSL 2.84 30 5138 278 93.22 0.19519 0.1911 0.26922 0.2453 RANDOM 47.297
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] -0.04 -0.02 -0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.519 r_dihedral_angle_4_deg 33.214 r_dihedral_angle_3_deg 17.776 r_dihedral_angle_1_deg 7.135 r_long_range_B_other 6.941 r_long_range_B_refined 6.94 r_scangle_other 4.661 r_mcangle_it 4.379 r_mcangle_other 4.378 r_scbond_it 2.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.519 r_dihedral_angle_4_deg 33.214 r_dihedral_angle_3_deg 17.776 r_dihedral_angle_1_deg 7.135 r_long_range_B_other 6.941 r_long_range_B_refined 6.94 r_scangle_other 4.661 r_mcangle_it 4.379 r_mcangle_other 4.378 r_scbond_it 2.911 r_scbond_other 2.91 r_mcbond_it 2.613 r_mcbond_other 2.612 r_angle_refined_deg 1.493 r_angle_other_deg 1.093 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1477 Nucleic Acid Atoms 410 Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing