4XDE

Coagulation Factor XII protease domain crystal structure


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.2 M Ammonium sulphate, 0.05 M tri-sodium citrate, 3%(w/v) isopropanol.
Crystal Properties
Matthews coefficientSolvent content
2.6453.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.126α = 90
b = 124.126β = 90
c = 38.145γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9763DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.1430.195.20.0852312.916670
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.142.199

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1YBW with 44% identity2.1430.11530181495.020.224180.222230.26235RANDOM29.211
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]
0.890.89-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.225
r_dihedral_angle_4_deg19.758
r_dihedral_angle_3_deg18.534
r_dihedral_angle_1_deg6.497
r_angle_other_deg3.851
r_angle_refined_deg1.855
r_chiral_restr0.146
r_bond_refined_d0.013
r_gen_planes_other0.009
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.225
r_dihedral_angle_4_deg19.758
r_dihedral_angle_3_deg18.534
r_dihedral_angle_1_deg6.497
r_angle_other_deg3.851
r_angle_refined_deg1.855
r_chiral_restr0.146
r_bond_refined_d0.013
r_gen_planes_other0.009
r_gen_planes_refined0.006
r_bond_other_d
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 AtomsNumber
Protein Atoms1829
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing