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SRPK1 bound to 9mer docking motif peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WAK PDB ENTRY 1WAK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 100MM SODIUM CITRATE PH5.6, 200MM AMMONIUM ACETATE, 15%PEG3350, 5MM PEPTIDE, 5MM ADP, 10MM MGCL2, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.99 58.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.68 α = 90 b = 78.68 β = 90 c = 310.54 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 105 CCD ADSC CCD 2003-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.4 30 97.8 0.07 8.1 11 22765 1 10.9
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 2.4 2.49 84 0.56 2.9 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WAK 2.4 28.26 2 15613 476 67.1 0.228 0.228 0.247 RANDOM 96.2
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] 21.3 14.59 21.3 -42.61
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_mcangle_it 11.44 c_scangle_it 10.7 c_mcbond_it 8.48 c_scbond_it 8.26 c_angle_deg 1.4 c_improper_angle_d 0.74 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_mcangle_it 11.44 c_scangle_it 10.7 c_mcbond_it 8.48 c_scbond_it 8.26 c_angle_deg 1.4 c_improper_angle_d 0.74 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2910 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 31
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing