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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 2W12 PDB ENTRY 2W12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 PEG 4000, NA(OAC), NH4(OAC), pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.1 α = 90 b = 59.6 β = 90 c = 82.7 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 1.14 20 98.7 0.07 18.8 6.9 68715 5 9.04
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 1.14 1.21 93 0.34 5.4
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 2W12 1.14 18.15 66242 2403 100 0.131 0.13 0.13 0.16 0.1583 RANDOM 9.09
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 38.164 r_dihedral_angle_4_deg 15.768 r_dihedral_angle_3_deg 11.271 r_dihedral_angle_1_deg 6.598 r_scangle_it 4.276 r_scbond_it 3.224 r_mcangle_it 2.442 r_mcbond_it 1.809 r_angle_refined_deg 1.776 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.164 r_dihedral_angle_4_deg 15.768 r_dihedral_angle_3_deg 11.271 r_dihedral_angle_1_deg 6.598 r_scangle_it 4.276 r_scbond_it 3.224 r_mcangle_it 2.442 r_mcbond_it 1.809 r_angle_refined_deg 1.776 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.303 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.121 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 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 345 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling