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Crystal structure of AaHIV, A metalloproteinase from venom of Agkistrodon Acutus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BUD PDB ENTRY 1BUD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 277 28% PEG400, 80mM calcium chloride, 0.1M HEPES sodium, pH7.5, EVAPORATION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.42 64.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.19 α = 90 b = 122.278 β = 90 c = 94.721 γ = 90
Symmetry Space Group C 2 2 21
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.100 BSRF 3W1A
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 2.3 50 95 0.084 10 5.1 25459
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 2.3 2.38 96.9 0.401 2.9 4.8 1479
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 1BUD 2.31 38.27 25459 1332 93.25 0.21427 0.21249 0.2158 0.24933 0.2209 RANDOM 39.943
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] 1.08 -0.99 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.418 r_dihedral_angle_3_deg 14.27 r_dihedral_angle_4_deg 10.832 r_dihedral_angle_1_deg 5.678 r_scangle_it 1.903 r_scbond_it 1.232 r_angle_refined_deg 1.111 r_mcangle_it 0.9 r_mcbond_it 0.554 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.418 r_dihedral_angle_3_deg 14.27 r_dihedral_angle_4_deg 10.832 r_dihedral_angle_1_deg 5.678 r_scangle_it 1.903 r_scbond_it 1.232 r_angle_refined_deg 1.111 r_mcangle_it 0.9 r_mcbond_it 0.554 r_nbtor_refined 0.298 r_nbd_refined 0.191 r_symmetry_hbond_refined 0.181 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.148 r_metal_ion_refined 0.146 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 3272 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 86
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling