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Human PRPF4B in complex with Rebastinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IJP PDB entry 4IJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 18% PEG Smear High, 0.1 M N-(2-acetamido)iminodiacetic acid, 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.69 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.169 α = 90 b = 75.661 β = 92.82 c = 68.075 γ = 90
Symmetry Space Group C 1 2 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 2017-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.968610 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 67.99 99.5 0.07 0.084 0.045 9.7 3.3 29242
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 99.5 0.535 0.638 0.344 2.4 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4IJP 2 67.99 27710 1351 99.38 0.18341 0.18221 0.1913 0.20591 0.2086 RANDOM 40.44
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] -1.01 -0.6 1.24 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.262 r_dihedral_angle_4_deg 16.948 r_dihedral_angle_3_deg 14.253 r_long_range_B_refined 5.979 r_long_range_B_other 5.918 r_dihedral_angle_1_deg 5.582 r_scangle_other 4.114 r_mcangle_it 2.994 r_mcangle_other 2.993 r_scbond_it 2.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.262 r_dihedral_angle_4_deg 16.948 r_dihedral_angle_3_deg 14.253 r_long_range_B_refined 5.979 r_long_range_B_other 5.918 r_dihedral_angle_1_deg 5.582 r_scangle_other 4.114 r_mcangle_it 2.994 r_mcangle_other 2.993 r_scbond_it 2.533 r_scbond_other 2.525 r_mcbond_it 2.001 r_mcbond_other 1.999 r_angle_refined_deg 1.27 r_angle_other_deg 0.924 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2580 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing