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Crystal structure of Danio rerio Slip1 in complex with Dbp5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.05 M MES pH 6.0, 18% (w/v) PEG 8000, 0.2 M Ca-Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.73 73.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.185 α = 90 b = 85.185 β = 90 c = 258.266 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2010-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.25 86.13 99.8 0.083 16.34 4.5 16724 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.45 99.9 0.68 2.3 4.6
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 2I2O 3.25 73.77 15869 836 100 0.245 0.244 0.2539 0.277 0.279 RANDOM 102.3
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] 5.92 2.96 5.92 -8.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.792 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_4_deg 14.176 r_dihedral_angle_1_deg 4.947 r_scangle_it 1.047 r_angle_refined_deg 0.985 r_mcangle_it 0.706 r_scbond_it 0.564 r_mcbond_it 0.382 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.792 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_4_deg 14.176 r_dihedral_angle_1_deg 4.947 r_scangle_it 1.047 r_angle_refined_deg 0.985 r_mcangle_it 0.706 r_scbond_it 0.564 r_mcbond_it 0.382 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3761 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling