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Monomeric Griffithsin with a Single Gly-Ser Insertion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 0.1 M sodium acetate, 0.15 M ammonium sulfate, 25% w/v PEG 3350, pH 4.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.6 α = 90 b = 48.6 β = 90 c = 94.2 γ = 120
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 2009-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1.1 30 97.9 0.063 13.7 6.2 48948
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) 1.1 1.12 99.7 0.583 3.5 2485
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HYR 1.11 25.17 2 48896 47848 1048 97.9 0.159 0.159 0.1649 0.159 0.1605 RANDOM 16.782
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] 0.09 0.05 0.09 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_4_deg 19.295 r_dihedral_angle_3_deg 11.516 r_dihedral_angle_1_deg 7.524 r_sphericity_bonded 6.104 r_scangle_it 4.965 r_scbond_it 4.218 r_mcangle_it 2.914 r_mcbond_it 2.442 r_rigid_bond_restr 2.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_4_deg 19.295 r_dihedral_angle_3_deg 11.516 r_dihedral_angle_1_deg 7.524 r_sphericity_bonded 6.104 r_scangle_it 4.965 r_scbond_it 4.218 r_mcangle_it 2.914 r_mcbond_it 2.442 r_rigid_bond_restr 2.396 r_angle_refined_deg 1.967 r_mcbond_other 1.867 r_angle_other_deg 1.013 r_symmetry_vdw_other 0.295 r_symmetry_vdw_refined 0.222 r_nbd_other 0.204 r_nbtor_refined 0.181 r_nbd_refined 0.167 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.12 r_nbtor_other 0.094 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 906 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 41
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling