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Crystal Structure of P13 Alanine Variant of Antithrombin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 Na/K Phosphate, PEG 4000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.14 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.998 α = 90 b = 98.573 β = 105.53 c = 89.35 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 100 AREA DETECTOR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.62 39.5 99.4 0.073 0.067 9 6.1 36632 35267 -3 76.609
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) Redundancy Number Unique Reflections (All) 1 2.62 2.74 96.4 0.496 0.453 3.2 5.9 5109
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1e04 2.62 39 36632 34900 1726 99.7 0.221 0.2228 0.258 0.2603 same as 1e04
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] -10.73 -7.66 20 -9.27
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_angle_deg 1.4 c_improper_angle_d 0.82 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6434 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 173
Software Software Software Name Purpose MAR345 data collection SCALA data scaling MOLREP phasing CNS refinement CCP4 data scaling