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Factor XA in complex with a cis-1,2-diaminocyclohexane derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 293 pH 5.00, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.055 α = 90 b = 72.179 β = 90 c = 79.238 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 IMAGE PLATE RIGAKU RAXIS IIC MONOCHROMATOR 2001-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.8 79.24 94.5 0.0484 2.66 28857
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) 1.8 1.86 78.3 0.266 2.26 2217
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 1FAX 1.8 25 26348 1375 96.22 0.20315 0.20164 0.192 0.23262 0.1886 RANDOM 30.392
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] 0.54 -0.83 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.192 r_dihedral_angle_4_deg 21.283 r_dihedral_angle_3_deg 12.871 r_dihedral_angle_1_deg 6.308 r_scangle_it 4.555 r_scbond_it 3.189 r_mcangle_it 2.003 r_angle_refined_deg 1.538 r_mcbond_it 1.101 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.192 r_dihedral_angle_4_deg 21.283 r_dihedral_angle_3_deg 12.871 r_dihedral_angle_1_deg 6.308 r_scangle_it 4.555 r_scbond_it 3.189 r_mcangle_it 2.003 r_angle_refined_deg 1.538 r_mcbond_it 1.101 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 2172 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PROCESS data reduction PROCESS data scaling REFMAC phasing