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Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B8W PDB Entry: 2B8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 20% Peg 3350, 130 mM NH4NO3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.921 α = 90 b = 173.45 β = 110.85 c = 49.632 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 CCD MAR CCD 165 mm 2002-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2.9 30 97.2 14479 -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 2.9 2.95 96.5
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: 2B8W 2.9 19.92 13093 13093 718 99.2 0.235 0.233 0.2242 0.275 0.2254 RANDOM 33.11
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] -0.07 -0.3 -1.38 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.111 r_scangle_it 1.592 r_mcangle_it 1.164 r_angle_refined_deg 0.964 r_scbond_it 0.854 r_mcbond_it 0.628 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.111 r_scangle_it 1.592 r_mcangle_it 1.164 r_angle_refined_deg 0.964 r_scbond_it 0.854 r_mcbond_it 0.628 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4611 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AMoRE phasing