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Matrix-metallopeptidase inhibitor Potempin A (PotA) from Tannerella forsythia in complex with T. forsythia karilysin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 The PotA:karilysin complex at 15 mg/mL in 50 mM sodium chloride, 5 mM calcium chloride, 0.02% sodium azide, 5 mM Tris-HCl pH 8.0 was crystallised from 25% (w/v) PEG 6,000, 100 mM MES, pH 6.0.
Crystal Properties Matthews coefficient Solvent content 2.05 39.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.24 α = 90 b = 62.94 β = 90 c = 108.68 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 PIXEL DECTRIS PILATUS3 6M 2016-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.35 62.9 98.6 0.06 0.063 1 20.8 12.4 57705 21.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.42 97.2 0.767 0.8 0.9 3.5 12.1
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 4IN9 1.35 36.07 57704 762 98.6 0.1545 0.1542 0.1535 0.1711 0.1708 RANDOM 22.28
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] -1.8346 1.5681 0.2665
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.58 t_omega_torsion 4.72 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.58 t_omega_torsion 4.72 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2065 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 56
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing