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Crystal Structure of 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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 293 PEG 6000, Tris-HCl, calcium chloride, pH 8, MICROBATCH, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.959 α = 90 b = 39.074 β = 99.56 c = 63.949 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 1.8 20 93.9 0.046 13.7 9.5 27532 27532 18.6
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) 1.8 1.88 72.4 0.252 2639
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 1IOD 1.8 19.54 27413 27413 2739 93.5 0.227 0.227 0.2278 0.27 0.2714 RANDOM 32.6
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] -8.41 2.32 7.69 0.72
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 2.86 c_mcangle_it 2.32 c_scbond_it 1.94 c_mcbond_it 1.47 c_angle_deg 1.2 c_improper_angle_d 0.69 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2480 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 10
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing