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Crystal structure of a complex of griffithsin cocrystallized with N-acetylglucosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.8M magnesium sulfate, 0.1M MES, 1:10 ratio of griffithsin monomers to N-acetylglucosamine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 39.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.57 α = 90 b = 53.41 β = 90 c = 104.01 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 MARMOSAIC 300 mm CCD 2006-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.564 50 98.8 0.084 4.7 30231 30231 -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 1.564 1.62 92.3
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2GUC 1.564 30 30231 28639 1531 99.36 0.16507 0.16507 0.16294 0.20512 0.1994 RANDOM 14.397
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] -0.08 -0.66 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.907 r_dihedral_angle_4_deg 23.648 r_dihedral_angle_3_deg 13.778 r_dihedral_angle_1_deg 7.2 r_scangle_it 4.636 r_scbond_it 3.383 r_angle_refined_deg 1.935 r_mcangle_it 1.888 r_mcbond_it 1.436 r_xyhbond_nbd_refined 0.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.907 r_dihedral_angle_4_deg 23.648 r_dihedral_angle_3_deg 13.778 r_dihedral_angle_1_deg 7.2 r_scangle_it 4.636 r_scbond_it 3.383 r_angle_refined_deg 1.935 r_mcangle_it 1.888 r_mcbond_it 1.436 r_xyhbond_nbd_refined 0.349 r_nbtor_refined 0.316 r_nbd_refined 0.276 r_symmetry_hbond_refined 0.264 r_symmetry_vdw_refined 0.218 r_chiral_restr 0.177 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1798 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 105
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling