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Factor Xa in complex with a phenylenediamine derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 macro-seeding, soak at pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.073 α = 90 b = 73.202 β = 90 c = 79.52 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 298 DIFFRACTOMETER WEISSENBERG monochromator 1999-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B 1.000 Photon Factory BL-6B
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 79.5 83.8 0.0468 23.8 4.88 19563 19561 -10
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 2.06 63.6 0.295 3.09 4.9 1322
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 rigid body refinement THROUGHOUT 3IIT 2 25 18301 949 98.83 0.19915 0.19825 0.1814 0.21628 0.1876 RANDOM 31.181
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] 0.76 -1.13 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.367 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 5.923 r_scangle_it 3.659 r_scbond_it 2.399 r_mcangle_it 1.709 r_angle_refined_deg 1.227 r_mcbond_it 0.892 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.367 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 5.923 r_scangle_it 3.659 r_scbond_it 2.399 r_mcangle_it 1.709 r_angle_refined_deg 1.227 r_mcbond_it 0.892 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2135 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 34
Software Software Software Name Purpose specificary data collection REFMAC refinement PROCESS data reduction PROCESS data scaling REFMAC phasing