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Crystal structure of recombinant coagulation factor beta-XIIa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292.15 0.1M Tris.Cl pH 8.0, 1.5M AmSO4
Crystal Properties Matthews coefficient Solvent content 3.69 66.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.932 α = 90 b = 106.932 β = 90 c = 65.962 γ = 90
Symmetry Space Group P 41 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 PILATUS 6M-F 2018-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.54 47.82 100 0.102 5.6 6.3 13130
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 2.54 2.61
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 4XDE 2.54 47.82 12479 620 99.93 0.2141 0.2115 0.2201 0.2636 0.2713 RANDOM 40.686
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] -1.74 -1.74 3.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.949 r_dihedral_angle_4_deg 20.897 r_dihedral_angle_3_deg 18.23 r_dihedral_angle_1_deg 7.961 r_angle_refined_deg 1.434 r_angle_other_deg 0.853 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.949 r_dihedral_angle_4_deg 20.897 r_dihedral_angle_3_deg 18.23 r_dihedral_angle_1_deg 7.961 r_angle_refined_deg 1.434 r_angle_other_deg 0.853 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1796 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing