3JTC

Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid Domains of Vitamin K-Dependent clotting and anticlotting Proteins


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7PEG 400, potassium chloride, magnesium chloride, calcium chloride, HEPES, PH 7.0, VAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
2.4349.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.22α = 90
b = 62.36β = 101.81
c = 71.03γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCHMIRRORS2001-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.553090.10.04127466375-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.61910.4550.043274

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.623.2256575302489.130.192460.190660.22648RANDOM25.75
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]
0.131.120.87-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.982
r_dihedral_angle_4_deg22.472
r_dihedral_angle_3_deg15.457
r_dihedral_angle_1_deg6.249
r_scangle_it5.371
r_scbond_it3.612
r_mcangle_it2.623
r_angle_refined_deg2.566
r_mcbond_it1.61
r_bond_refined_d1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.982
r_dihedral_angle_4_deg22.472
r_dihedral_angle_3_deg15.457
r_dihedral_angle_1_deg6.249
r_scangle_it5.371
r_scbond_it3.612
r_mcangle_it2.623
r_angle_refined_deg2.566
r_mcbond_it1.61
r_bond_refined_d1.45
r_nbtor_refined0.304
r_nbd_refined0.245
r_symmetry_vdw_refined0.21
r_chiral_restr0.173
r_metal_ion_refined0.155
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.118
r_gen_planes_refined0.032
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 AtomsNumber
Protein Atoms3422
Nucleic Acid Atoms
Solvent Atoms407
Heterogen Atoms198

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling