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Crystal structure of human prethrombin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E6P PDB entry 3E6P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 100mM Tris-HCl, pH 8.5 and 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.54 51.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.893 α = 90 b = 81.006 β = 90 c = 88.463 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2010-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
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 2.2 40 95.5 0.109 9.5 3.2 25400 24257 -0.5 -0.5
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) 2.2 2.28 94.5 0.39 2.4 3.2 2351
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3E6P 2.2 59.74 -0.5 24078 22995 1244 95.5 0.19895 0.1975 0.1963 0.2255 0.2272 RANDOM
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] -0.24 -2.75 2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.795 r_dihedral_angle_3_deg 16.88 r_dihedral_angle_4_deg 15.029 r_dihedral_angle_1_deg 6.105 r_scangle_it 2.498 r_scbond_it 1.594 r_angle_refined_deg 1.331 r_mcangle_it 0.887 r_mcbond_it 0.465 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.795 r_dihedral_angle_3_deg 16.88 r_dihedral_angle_4_deg 15.029 r_dihedral_angle_1_deg 6.105 r_scangle_it 2.498 r_scbond_it 1.594 r_angle_refined_deg 1.331 r_mcangle_it 0.887 r_mcbond_it 0.465 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3112 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 42
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling