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Crystal structure of Echistatin, an RGD-containing short disintegrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Bicine pH9.0
2.55M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 1.8 31.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.906 α = 90 b = 33.906 β = 90 c = 121.172 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 RAYONIX MX300-HS 2016-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
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 1.8 30 92.5 0.991 7.88 4.9 7695
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 1.8 1.91 0.951 2.96
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 4RQG 1.8 30 7541 419 99.29 0.21226 0.212 0.2193 0.255 0.2565 RANDOM 28.851
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 0.47 0.93 -3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_4_deg 10.857 r_dihedral_angle_1_deg 6.889 r_long_range_B_refined 5.404 r_long_range_B_other 5.4 r_scangle_other 4.265 r_mcangle_it 2.646 r_mcangle_other 2.644 r_scbond_it 2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_4_deg 10.857 r_dihedral_angle_1_deg 6.889 r_long_range_B_refined 5.404 r_long_range_B_other 5.4 r_scangle_other 4.265 r_mcangle_it 2.646 r_mcangle_other 2.644 r_scbond_it 2.61 r_scbond_other 2.608 r_mcbond_it 1.789 r_mcbond_other 1.787 r_angle_refined_deg 1.461 r_angle_other_deg 1.333 r_chiral_restr 0.087 r_gen_planes_refined 0.014 r_bond_refined_d 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 758 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling XDS phasing