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Crystal structure of the Xenopus tropicalis Spred1 EVH-1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EVH PDB entry 1EVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 PEG 3350, potassium fluoride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.94 36.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.881 α = 90 b = 38.267 β = 95.58 c = 80.226 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2004-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.65 25 96.2 0.052 0.052 38.2 6.2 24189 23273 16.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.65 1.69 94.6 0.211 0.211 9.35 5.7 1497
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1EVH 1.65 25 24189 23262 1188 96.08 0.1539 0.1539 0.151 0.1578 0.181 RANDOM 13.099
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] 0.37 -0.06 -0.5 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.797 r_scangle_it 4.035 r_scbond_it 2.402 r_mcangle_it 1.695 r_angle_refined_deg 1.507 r_mcbond_it 0.954 r_angle_other_deg 0.856 r_symmetry_vdw_other 0.347 r_nbd_other 0.266 r_symmetry_vdw_refined 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.797 r_scangle_it 4.035 r_scbond_it 2.402 r_mcangle_it 1.695 r_angle_refined_deg 1.507 r_mcbond_it 0.954 r_angle_other_deg 0.856 r_symmetry_vdw_other 0.347 r_nbd_other 0.266 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.183 r_nbtor_other 0.128 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 1706 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing