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Three-Dimensional Structure of a Llama VHH Domain OE7 binding the cell wall protein Malf1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HCV PDB entry 1HCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 10% PEG 6K, 100mM Hepes, 5% MPD, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.17 70.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.4 α = 90 b = 71.4 β = 90 c = 74.84 γ = 120
Symmetry Space Group P 32 2 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 CCD ADSC QUANTUM 4 2000-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9326 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 24 99.8 0.042 0.042 3.5 11594 3.5 3.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 99.8 0.2 0.2 3.5 6 1637
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 (All) 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 1HCV 2.2 24 2 10773 10763 804 99.87 0.2 0.19163 0.19054 0.1864 0.20644 0.2001 RANDOM 22.713
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.508 r_scangle_it 2.561 r_scbond_it 1.56 r_angle_refined_deg 1.28 r_mcangle_it 1.049 r_mcbond_it 0.536 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.508 r_scangle_it 2.561 r_scbond_it 1.56 r_angle_refined_deg 1.28 r_mcangle_it 1.049 r_mcbond_it 0.536 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 900 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling AMoRE phasing