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Atomic-resolution crystal structure of the natural form of Scytovirin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 293 30% PEG 8000, 0.2M Li2SO4, 0.1M Na Acetate, pH 4.7, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.48 α = 90 b = 38.84 β = 90 c = 59.72 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 210 2002-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 0.979 NSLS X9B
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 1.3 25 99.2 0.082 12.3 5.6 21876
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.3 1.35 95.8 4.5 2080
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.3 19.42 20294 939 92.87 0.147 0.145 0.1542 0.198 0.2049 RANDOM 12.744
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 0.33 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.363 r_dihedral_angle_3_deg 11.322 r_dihedral_angle_1_deg 6.512 r_sphericity_bonded 6.3 r_dihedral_angle_4_deg 5.33 r_scangle_it 4.426 r_scbond_it 4.242 r_mcangle_it 4.016 r_mcbond_it 3.532 r_rigid_bond_restr 3.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.363 r_dihedral_angle_3_deg 11.322 r_dihedral_angle_1_deg 6.512 r_sphericity_bonded 6.3 r_dihedral_angle_4_deg 5.33 r_scangle_it 4.426 r_scbond_it 4.242 r_mcangle_it 4.016 r_mcbond_it 3.532 r_rigid_bond_restr 3.105 r_mcbond_other 1.739 r_angle_refined_deg 1.525 r_angle_other_deg 1.035 r_symmetry_vdw_other 0.271 r_xyhbond_nbd_refined 0.227 r_nbd_refined 0.206 r_nbd_other 0.206 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.149 r_symmetry_vdw_refined 0.142 r_chiral_restr 0.1 r_nbtor_other 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 699 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection SHELXS phasing