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Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ANY PDB ENTRY 2ANY AND 3IDX experimental model PDB 3IDX PDB ENTRY 2ANY AND 3IDX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 FAB DX-2930 AND HUMAN PLASMA KALLIKREIN VCID 7481 AT 150 UM OR 11.7 MG/ML AGAINST INDEX screen condition D10, 20% PEG 5000 MME, 0.1 M BisTris pH 6.5 supplemented with 20% ethylene glycol as cryo-protectant, unique puck ID qjo1-15, crystal tracking ID 242121d10, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.12 α = 90 b = 113.76 β = 94.7 c = 89.05 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 944+ VARIMAX 2013-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.1 50 99.8 0.076 22.6 7.3 95084 94897 -3 28.24
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 2.1 2.14 98.8 0.346 5.8 6.1
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 PDB ENTRY 2ANY AND 3IDX 2.1 40.59 94873 4757 99.82 0.185 0.183 0.1901 0.221 0.2281 RANDOM 26.51
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] 0.31 -0.07 -0.15 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.178 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 13.144 r_dihedral_angle_1_deg 6.553 r_mcangle_it 1.441 r_angle_refined_deg 1.361 r_angle_other_deg 0.954 r_mcbond_it 0.807 r_mcbond_other 0.807 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.178 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 13.144 r_dihedral_angle_1_deg 6.553 r_mcangle_it 1.441 r_angle_refined_deg 1.361 r_angle_other_deg 0.954 r_mcbond_it 0.807 r_mcbond_other 0.807 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_scbond_it 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 9991 Nucleic Acid Atoms Solvent Atoms 1020 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction