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STRUCTURE OF HUMAN IGF2R DOMAINS 11-14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V5N PDB ENTRY 2V5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.4 0.1 M MES PH6.4, 2.5% (W/V) PEG 3000
Crystal Properties Matthews coefficient Solvent content 3.3 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.554 α = 90 b = 69.247 β = 103.25 c = 98.012 γ = 90
Symmetry Space Group C 1 2 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 MARRESEARCH TOROIDAL MIRROR 2004-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.9 30 98.6 0.08 13.9 3.7 19919 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 92.8 0.5 3 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 2V5N 2.91 28.46 18893 1024 99.3 0.259 0.257 0.265 0.304 0.3019 RANDOM 65.81
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] 1.01 5.39 -3.31 4.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.395 r_dihedral_angle_3_deg 18.579 r_dihedral_angle_4_deg 12.974 r_dihedral_angle_1_deg 6.782 r_angle_refined_deg 1.164 r_nbtor_refined 0.306 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.395 r_dihedral_angle_3_deg 18.579 r_dihedral_angle_4_deg 12.974 r_dihedral_angle_1_deg 6.782 r_angle_refined_deg 1.164 r_nbtor_refined 0.306 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4642 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing