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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 2DSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 290 20% PEG 3350, 0.2M lithium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.22 44.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.28 α = 90 b = 43.66 β = 91.67 c = 81.15 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 2006-04-22 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 2.8 20 99 14042 13980 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) 2.8 2.9 92
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DSP 2.8 10 2 14042 11658 618 99.85 0.29188 0.28845 0.35708 RANDOM 59.895
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] -2.5 -0.23 6.26 -3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.148 r_dihedral_angle_3_deg 20.11 r_dihedral_angle_4_deg 19.052 r_dihedral_angle_1_deg 6.272 r_angle_refined_deg 1.154 r_symmetry_hbond_refined 0.385 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.148 r_dihedral_angle_3_deg 20.11 r_dihedral_angle_4_deg 19.052 r_dihedral_angle_1_deg 6.272 r_angle_refined_deg 1.154 r_symmetry_hbond_refined 0.385 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3072 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing