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SRPK1 in complex with Alectinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WAK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 11% PEG 4000
100mM sodium citrate (pH 5.6)
200mM ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.95 58.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.767 α = 90 b = 74.767 β = 90 c = 310.687 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 315r Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , Toroidal Focusing Mirror 2016-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.32 63.39 99.1 33.67 13.6 316057
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 1WAK 2.32 63.39 22080 1195 99.53 0.21345 0.21211 0.2171 0.23797 0.2381 RANDOM 41.743
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] 0.03 0.01 0.03 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.319 r_dihedral_angle_4_deg 18.91 r_dihedral_angle_3_deg 14.69 r_long_range_B_refined 6.09 r_long_range_B_other 6.089 r_dihedral_angle_1_deg 5.759 r_scangle_other 4.435 r_mcangle_it 3.046 r_mcangle_other 3.045 r_scbond_it 2.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.319 r_dihedral_angle_4_deg 18.91 r_dihedral_angle_3_deg 14.69 r_long_range_B_refined 6.09 r_long_range_B_other 6.089 r_dihedral_angle_1_deg 5.759 r_scangle_other 4.435 r_mcangle_it 3.046 r_mcangle_other 3.045 r_scbond_it 2.674 r_scbond_other 2.673 r_mcbond_it 1.913 r_mcbond_other 1.911 r_angle_refined_deg 1.395 r_angle_other_deg 0.898 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_bond_other_d 0.007 r_gen_planes_refined 0.005 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 2849 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data processing Coot model building PHASER phasing