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Crystal structure of Danio rerio Lin41 filamin-NHL domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UMG Homology models based on PDB IDs 4UMG and 1Q7F experimental model PDB 1Q7F Homology models based on PDB IDs 4UMG and 1Q7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 10% PEG 8000
0.2 M magnesium chloride
0.1 M Tris pH 7.0
0.1 M trisodium citrate
Crystal Properties Matthews coefficient Solvent content 2.19 43.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.8 α = 90 b = 90.59 β = 90 c = 131.05 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.260 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.6 50 91.6 0.124 0.987 5.28 1.9 42647 45.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 86.8 0.491 0.779 1.8
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 Homology models based on PDB IDs 4UMG and 1Q7F 2.6 46.43 23630 1182 95.35 0.1847 0.1815 0.1991 0.2439 0.2695 RANDOM 30.59
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] -3.2829 -2.6882 5.9711
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.13 t_omega_torsion 3.06 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.13 t_omega_torsion 3.06 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6002 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing