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High-resolution crystal structure of the P-I snake venom metalloproteinase BaP1 in complex with a peptidomimetic: insights into inhibitor binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W14 PDB ENTRY 2W14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PEG 3000, HEPES, NACL, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.9 α = 90 b = 59.8 β = 90 c = 83.3 γ = 90
Symmetry Space Group P 21 21 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.05 20 95 0.05 25.2 7.6 84722 5 10.1
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 1.05 1.11 75.9 0.22 7.8
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 2W14 1.05 19.67 82161 2542 100 0.117 0.116 0.1168 0.143 0.1441 RANDOM 9.15
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_2_deg 37.804 r_dihedral_angle_4_deg 17.053 r_dihedral_angle_3_deg 10.779 r_dihedral_angle_1_deg 6.33 r_scangle_it 4.647 r_scbond_it 3.698 r_mcangle_it 3.139 r_mcbond_it 2.351 r_angle_refined_deg 1.793 r_symmetry_vdw_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.804 r_dihedral_angle_4_deg 17.053 r_dihedral_angle_3_deg 10.779 r_dihedral_angle_1_deg 6.33 r_scangle_it 4.647 r_scbond_it 3.698 r_mcangle_it 3.139 r_mcbond_it 2.351 r_angle_refined_deg 1.793 r_symmetry_vdw_refined 0.338 r_nbtor_refined 0.31 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.125 r_symmetry_hbond_refined 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 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_refined 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_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 1598 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling