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Crystal structure of LOV2 (C450A) domain in complex with Zdk2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WKQ 2WKQ and a homology model based on 2KZJ experimental model PDB 2KZJ 2WKQ and a homology model based on 2KZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M tri-sodium citrate pH 5.6, 0.2 M ammonium acetate, 32% (w/v) PEG 4000 and 0.1 M copper(II) chloride as an additive
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.14 α = 90 b = 110.14 β = 90 c = 37.51 γ = 90
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 2014-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00005 SLS X10SA
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 1.4 50 99.6 0.065 15.5 5.7 44465
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 1.4 1.5 99.7 0.36 4.2 5.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2WKQ and a homology model based on 2KZJ 1.4 35.507 1.4 44463 2223 99.62 0.1471 0.1458 0.1515 0.171 0.1744
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 f_dihedral_angle_d 15.917 f_angle_d 1.343 f_chiral_restr 0.093 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing