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Crystal structure of nanoCLAMP3:VHH in complex with MTX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QXV 3QXV 2W1Q experimental model PDB 2W1Q 3QXV 2W1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.4 M sodium malonate-malonic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 5.49 77.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.2 α = 90 b = 143.969 β = 94.34 c = 181.814 γ = 90
Symmetry Space Group I 1 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 MARMOSAIC 225 mm CCD 2020-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.9 48.38 100 1 7.5 14.2 1401844
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.975 100 1 14.5
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 3QXV 2W1Q 2.9 48.38 93544 4949 99.96 0.1971 0.19469 0.1994 0.24223 0.2404 RANDOM 73.108
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] 2.91 -0.42 0.05 -3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.741 r_dihedral_angle_3_deg 21.713 r_dihedral_angle_4_deg 20.377 r_dihedral_angle_1_deg 7.921 r_scangle_it 4.204 r_scbond_it 2.421 r_angle_refined_deg 2.057 r_mcangle_it 1.835 r_mcbond_it 0.949 r_chiral_restr 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.741 r_dihedral_angle_3_deg 21.713 r_dihedral_angle_4_deg 20.377 r_dihedral_angle_1_deg 7.921 r_scangle_it 4.204 r_scbond_it 2.421 r_angle_refined_deg 2.057 r_mcangle_it 1.835 r_mcbond_it 0.949 r_chiral_restr 0.137 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14416 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 245
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing