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Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 297 0.1M BIS-TRIS propane pH 8.5, 24% PEG 3350, 0.275M Na Malonate
Crystal Properties Matthews coefficient Solvent content 3.42 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.16 α = 90 b = 100.16 β = 90 c = 91.5 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 PIXEL DECTRIS PILATUS3 R CdTe 300K 2015-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 70.82 99.9 13.9 7.5 61775
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63
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 5JB8 1.6 70.82 58601 3114 99.83 0.12792 0.12607 0.1395 0.16314 0.1733 RANDOM 33.236
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] -0.33 -0.33 0.66
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.283 r_dihedral_angle_2_deg 32.826 r_sphericity_bonded 20.348 r_dihedral_angle_4_deg 16.625 r_dihedral_angle_3_deg 11.522 r_scangle_other 9.419 r_long_range_B_other 8.664 r_long_range_B_refined 8.65 r_scbond_it 8.639 r_scbond_other 8.637
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.283 r_dihedral_angle_2_deg 32.826 r_sphericity_bonded 20.348 r_dihedral_angle_4_deg 16.625 r_dihedral_angle_3_deg 11.522 r_scangle_other 9.419 r_long_range_B_other 8.664 r_long_range_B_refined 8.65 r_scbond_it 8.639 r_scbond_other 8.637 r_rigid_bond_restr 7.282 r_mcangle_other 6.722 r_mcangle_it 6.721 r_dihedral_angle_1_deg 6.393 r_mcbond_it 5.937 r_mcbond_other 5.851 r_angle_refined_deg 2.656 r_angle_other_deg 2.462 r_chiral_restr 0.2 r_bond_refined_d 0.033 r_gen_planes_refined 0.014 r_gen_planes_other 0.014 r_bond_other_d 0.003 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2264 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing