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Crystal Structure of FXa in complex with 4,4-disubstituted pyrrolidine-1,2-dicarboxamide inhibitor 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PHB PDB ENTRY 2PHB
Crystallization Crystal Properties Matthews coefficient Solvent content 2.4 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.359 α = 90 b = 72.503 β = 90 c = 78.399 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 ADSC CCD 2004-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 2.05 20 96.1 0.06 19.34 5.59 19989
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 2.05 2.12 83 0.32 3.6 4.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PHB 2.05 50 18924 1032 96.6 0.211 0.208 0.2127 0.255 RANDOM 28.22
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] -0.02 -1.83 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.88 r_dihedral_angle_4_deg 21.327 r_dihedral_angle_3_deg 15.638 r_dihedral_angle_1_deg 6.051 r_scangle_it 1.888 r_scbond_it 1.219 r_angle_refined_deg 1.205 r_mcangle_it 0.971 r_angle_other_deg 0.819 r_mcbond_it 0.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.88 r_dihedral_angle_4_deg 21.327 r_dihedral_angle_3_deg 15.638 r_dihedral_angle_1_deg 6.051 r_scangle_it 1.888 r_scbond_it 1.219 r_angle_refined_deg 1.205 r_mcangle_it 0.971 r_angle_other_deg 0.819 r_mcbond_it 0.586 r_symmetry_vdw_other 0.282 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.211 r_nbd_other 0.188 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.107 r_nbtor_other 0.083 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2225 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing