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Aminopyrrolidine Factor Xa inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VVC PDB ENTRY 2VVC
Crystallization Crystal Properties Matthews coefficient Solvent content 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.54 α = 90 b = 105.54 β = 90 c = 49.79 γ = 90
Symmetry Space Group P 43 21 2
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 2005-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.61 50 99.4 0.05 22.8 7.2 36756 -3
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 1.61 1.7 100 0.36 5.85 6.75
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 2VVC 1.61 74.54 34921 1835 99.4 0.193 0.191 0.1935 0.228 0.229 RANDOM 25.79
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.275 r_dihedral_angle_4_deg 15.012 r_dihedral_angle_3_deg 11.833 r_dihedral_angle_1_deg 5.579 r_scangle_it 3.082 r_scbond_it 1.966 r_mcangle_it 1.412 r_angle_refined_deg 1.381 r_mcbond_it 0.796 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.275 r_dihedral_angle_4_deg 15.012 r_dihedral_angle_3_deg 11.833 r_dihedral_angle_1_deg 5.579 r_scangle_it 3.082 r_scbond_it 1.966 r_mcangle_it 1.412 r_angle_refined_deg 1.381 r_mcbond_it 0.796 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 2175 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing