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Crystal structure of a Human Factor Xa inhibitor complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other SEE REMARK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.75 18% PEG 6K, 100MM MES PH5.75, 10MM CACL2
Crystal Properties Matthews coefficient Solvent content 2.45 49.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.968 α = 90 b = 72.633 β = 90 c = 79.784 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 2001-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 30 99.8 0.08 4.04 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 2.1 2.18 0.53
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SEE REMARK 2.1 20 18829 1015 100 0.195 0.192 0.242 0.2391 RANDOM 32.68
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] 0.43 -1.69 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.406 r_dihedral_angle_4_deg 17.578 r_dihedral_angle_3_deg 11.103 r_scangle_it 5.12 r_dihedral_angle_1_deg 3.98 r_scbond_it 3.851 r_mcangle_it 2.825 r_mcbond_it 1.723 r_angle_refined_deg 1.58 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.406 r_dihedral_angle_4_deg 17.578 r_dihedral_angle_3_deg 11.103 r_scangle_it 5.12 r_dihedral_angle_1_deg 3.98 r_scbond_it 3.851 r_mcangle_it 2.825 r_mcbond_it 1.723 r_angle_refined_deg 1.58 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 2148 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling