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Crystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP/AlF4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F5N PDB ENTRY 1F5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 5% PEG3350, 150 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.01 59.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.617 α = 90 b = 101.927 β = 90 c = 54.121 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 4 2002-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.22 30 98.4 0.078 20.6 14.05 41099 -3 38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.25 97.7 0.485 5.5 13.4
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 (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 1F5N 2.22 29.75 38814 38814 2758 99.6 0.193 0.19 0.2006 0.233 0.2393 RANDOM 31.22
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] -1.36 -0.76 2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.297 r_dihedral_angle_4_deg 24.582 r_dihedral_angle_3_deg 20.79 r_dihedral_angle_1_deg 8.735 r_scangle_it 6.814 r_scbond_it 5.09 r_mcangle_it 3.057 r_mcbond_it 2.39 r_angle_refined_deg 0.781 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.297 r_dihedral_angle_4_deg 24.582 r_dihedral_angle_3_deg 20.79 r_dihedral_angle_1_deg 8.735 r_scangle_it 6.814 r_scbond_it 5.09 r_mcangle_it 3.057 r_mcbond_it 2.39 r_angle_refined_deg 0.781 r_nbtor_refined 0.323 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.219 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.067 r_gen_planes_refined 0.03 r_bond_refined_d 0.007 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_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 4582 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AMoRE phasing