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Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A2Q PDB ENTRY 2A2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 20% PEG 4000, 50 mM Tris-HCL, 50 mM N-(2-Acetamido)iminodiacetic acid, 150 mM NaCl, 2.5 mM Calcium Chloride, 1.25 mM Magnesium Chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.14 60.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.079 α = 90 b = 68.894 β = 91.19 c = 79.153 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 315 2006-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 55.01 98.8 0.125 0.1 9.98 3.4 22917 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 2A2Q 2.7 55.01 2 21733 1184 98.4 0.232 0.228 0.2253 0.298 0.2907 RANDOM 47.43
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] -0.02 0.02 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.103 r_dihedral_angle_3_deg 21.821 r_dihedral_angle_4_deg 15.934 r_dihedral_angle_1_deg 7.45 r_scangle_it 3.654 r_scbond_it 2.172 r_angle_refined_deg 1.85 r_mcangle_it 1.596 r_mcbond_it 0.83 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.103 r_dihedral_angle_3_deg 21.821 r_dihedral_angle_4_deg 15.934 r_dihedral_angle_1_deg 7.45 r_scangle_it 3.654 r_scbond_it 2.172 r_angle_refined_deg 1.85 r_mcangle_it 1.596 r_mcbond_it 0.83 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 3934 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 65
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling