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Crystal structure of cyanovirin-n complexed to a synthetic hexamannoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZM PDB entry 3EZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.3 298 0.1M CHES, 1M NaCitrate, pH 10.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.15 60.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.352 α = 90 b = 61.352 β = 90 c = 147.568 γ = 90
Symmetry Space Group P 41 21 2
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 4 mirror 2001-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 1.0 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 2.4 40 99.8 0.056 11728 44.6
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 2.4 2.49 99.6
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 3EZM 2.4 19.92 11069 555 100 0.21102 0.20807 0.2155 0.271 0.2684 RANDOM 21.982
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] -0.93 -0.93 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.526 r_dihedral_angle_4_deg 23.397 r_dihedral_angle_3_deg 16.93 r_dihedral_angle_1_deg 6.629 r_scangle_it 3.741 r_scbond_it 2.331 r_angle_refined_deg 2.196 r_mcangle_it 1.383 r_mcbond_it 0.719 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.526 r_dihedral_angle_4_deg 23.397 r_dihedral_angle_3_deg 16.93 r_dihedral_angle_1_deg 6.629 r_scangle_it 3.741 r_scbond_it 2.331 r_angle_refined_deg 2.196 r_mcangle_it 1.383 r_mcbond_it 0.719 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1540 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 92
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling