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Crystal structure of microtubule binding domain of human EB3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 298 0.04M potassium phosphate, 16% PEG 8000, 20% glycerol anhydrous, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.188 α = 90 b = 85.365 β = 90 c = 32.161 γ = 90
Symmetry Space Group P 21 21 2
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 PSI PILATUS 6M 2007-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0090 SLS X06SA
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 1.4 50 96.9 0.107 10.85 25525 25525 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 92.9
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1PA7 1.4 42.68 24229 24229 1296 96.87 0.20161 0.20161 0.20001 0.2001 0.23355 0.2306 RANDOM 11.734
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] -0.57 0.62 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.137 r_dihedral_angle_3_deg 12.346 r_dihedral_angle_4_deg 11.078 r_scangle_it 6.39 r_dihedral_angle_1_deg 4.494 r_scbond_it 4.441 r_mcangle_it 2.698 r_mcbond_it 1.936 r_angle_refined_deg 1.067 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.137 r_dihedral_angle_3_deg 12.346 r_dihedral_angle_4_deg 11.078 r_scangle_it 6.39 r_dihedral_angle_1_deg 4.494 r_scbond_it 4.441 r_mcangle_it 2.698 r_mcbond_it 1.936 r_angle_refined_deg 1.067 r_nbtor_refined 0.309 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1083 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction XSCALE data scaling PHASER phasing