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Crystal structure of SRPK1 in complex with a peptide inhibitor
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 289.15 3% PEG 3350, 200mM Ammonium acetata, 100mM Sodium Citrate(pH 5.6), 4mM DTT
Crystal Properties Matthews coefficient Solvent content 2.75 55.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.042 α = 90 b = 75.042 β = 90 c = 313.175 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 110 CCD RAYONIX MX300-HS 2017-04-03 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) 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 2.05 30.03 99.9 0.057 101.35 20.6 32136
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 0.057
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 2.05 30.03 32136 1690 99.83 0.1822 0.1802 0.1932 0.2205 0.2308 RANDOM 28.642
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.684 r_dihedral_angle_4_deg 21.166 r_dihedral_angle_3_deg 15.117 r_dihedral_angle_1_deg 6.605 r_angle_refined_deg 1.673 r_angle_other_deg 1.367 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.684 r_dihedral_angle_4_deg 21.166 r_dihedral_angle_3_deg 15.117 r_dihedral_angle_1_deg 6.605 r_angle_refined_deg 1.673 r_angle_other_deg 1.367 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2893 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALA data scaling