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Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 23% PEG 1500, 25mM Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.18 43.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.33 α = 90 b = 38.99 β = 99.89 c = 61.33 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 MAR scanner 345 mm plate Monochromator 2004-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 30 96 5354 5177 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.6 87
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1WQJ 2.5 20 2 5177 5086 243 99.98 0.22269 0.22046 0.2197 0.27094 0.272 RANDOM 40.482
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] 0.41 0.63 -0.96 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.775 r_dihedral_angle_3_deg 19.028 r_dihedral_angle_4_deg 14.219 r_dihedral_angle_1_deg 6.641 r_scangle_it 2.075 r_angle_refined_deg 1.37 r_scbond_it 1.265 r_mcangle_it 1.019 r_mcbond_it 0.629 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.775 r_dihedral_angle_3_deg 19.028 r_dihedral_angle_4_deg 14.219 r_dihedral_angle_1_deg 6.641 r_scangle_it 2.075 r_angle_refined_deg 1.37 r_scbond_it 1.265 r_mcangle_it 1.019 r_mcbond_it 0.629 r_nbtor_refined 0.297 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1067 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing