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Crystal structure of X. tropicalis Spred1 EVH-1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EVH pdb entries 1EVH, 1I7A, 1QC6 experimental model PDB 1I7A pdb entries 1EVH, 1I7A, 1QC6 experimental model PDB 1QC6 pdb entries 1EVH, 1I7A, 1QC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 PEG 3350, potassium fluoride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.92 35.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.811 α = 90 b = 38.193 β = 95.68 c = 79.907 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 4 mirrors 2004-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.975 SRS PX14.2
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 1.15 79 97.7 0.069 19.4 3.9 68977 68977 7.84
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 1.15 1.17 94.5 0.351 3.99 3.5 3330
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entries 1EVH, 1I7A, 1QC6 1.15 79.06 68977 68977 3471 97.69 0.155 0.15538 0.154 0.177 random 9.283
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] 0.13 -0.17 0.06 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.147 r_scangle_it 2.68 r_sphericity_free 2.217 r_sphericity_bonded 1.855 r_scbond_it 1.752 r_mcangle_it 1.536 r_angle_refined_deg 1.335 r_rigid_bond_restr 0.947 r_mcbond_it 0.94 r_angle_other_deg 0.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.147 r_scangle_it 2.68 r_sphericity_free 2.217 r_sphericity_bonded 1.855 r_scbond_it 1.752 r_mcangle_it 1.536 r_angle_refined_deg 1.335 r_rigid_bond_restr 0.947 r_mcbond_it 0.94 r_angle_other_deg 0.833 r_symmetry_vdw_refined 0.487 r_symmetry_vdw_other 0.324 r_nbd_other 0.26 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.196 r_xyhbond_nbd_refined 0.171 r_nbtor_other 0.085 r_chiral_restr 0.079 r_gen_planes_other 0.019 r_gen_planes_refined 0.012 r_bond_refined_d 0.009 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1694 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing