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Crystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IOD PDB ENTRY 1IOD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 293 PEG 6000, Tris-HCl, calcium chloride, magnesium chloride, pH 8, MICROBATCH, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.77 29.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.552 α = 90 b = 37.204 β = 103.56 c = 62.626 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2001-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.72 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 20 93.6 0.037 10.7 9 39489 39489 -0.5 17.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.55 1.65 63.3 0.209 3302
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1IOD 1.55 19.63 38082 38082 3811 90.1 0.185 0.183 0.1834 0.212 0.2122 RANDOM 22.8
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] -5.85 3.39 2.24 3.61
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 2.89 c_mcangle_it 1.94 c_scbond_it 1.94 c_angle_deg 1.3 c_mcbond_it 1.24 c_improper_angle_d 0.69 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2480 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 10
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing