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Crystal Structure of a Five Site Mutated Cyanovirin-N with a Mannose Dimer Bound at 1.8 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LOM pdb entry 1LOM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 30% PEG 8000, 100 MM MGSO4, 2 MM MAN2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.226 α = 90 b = 38.281 β = 99.69 c = 55.794 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 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2005-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.8 55.22 87.7 0.094 8.13 1.9 19361 4
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) 1.8 1.85 82.33 0.244 2.92 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1LOM 1.8 9.99 17236 924 94.5 0.171 0.169 0.1912 0.215 0.1827 RANDOM 22.49
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] 0.05 -0.04 0.08 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.064 r_dihedral_angle_4_deg 15.907 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_1_deg 6.977 r_sphericity_free 6.754 r_scangle_it 4.11 r_scbond_it 3.53 r_sphericity_bonded 2.364 r_rigid_bond_restr 2.254 r_mcangle_it 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.064 r_dihedral_angle_4_deg 15.907 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_1_deg 6.977 r_sphericity_free 6.754 r_scangle_it 4.11 r_scbond_it 3.53 r_sphericity_bonded 2.364 r_rigid_bond_restr 2.254 r_mcangle_it 1.83 r_mcbond_it 1.753 r_angle_refined_deg 1.733 r_angle_other_deg 1.389 r_mcbond_other 0.449 r_xyhbond_nbd_refined 0.284 r_nbd_refined 0.218 r_chiral_restr 0.212 r_symmetry_vdw_other 0.21 r_nbd_other 0.209 r_symmetry_vdw_refined 0.176 r_nbtor_refined 0.168 r_symmetry_hbond_refined 0.107 r_nbtor_other 0.092 r_bond_other_d 0.029 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1539 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 46
Software Software Software Name Purpose PHASER phasing REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling