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Crystal structure of native protein C activator from the venom of copperhead snake Agkistrodon contortrix contortrix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BQY PDB entry 1BQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.867 α = 90 b = 63.295 β = 99.8 c = 48.237 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 2005-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.438 LNLS D03B-MX1
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 1.65 19.03 99.8 0.09 28664 2.5 2.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 99.6
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 (All) 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 1BQY 1.65 19.03 2.5 27223 1440 99.49 0.1743 0.17086 0.16949 0.1699 0.19692 0.1756 RANDOM 21.121
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.602 r_dihedral_angle_4_deg 18.61 r_dihedral_angle_3_deg 12.548 r_dihedral_angle_1_deg 6.219 r_scangle_it 2.999 r_scbond_it 2.03 r_angle_refined_deg 1.493 r_mcangle_it 1.393 r_mcbond_it 0.802 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.602 r_dihedral_angle_4_deg 18.61 r_dihedral_angle_3_deg 12.548 r_dihedral_angle_1_deg 6.219 r_scangle_it 2.999 r_scbond_it 2.03 r_angle_refined_deg 1.493 r_mcangle_it 1.393 r_mcbond_it 0.802 r_nbtor_refined 0.323 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.2 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1757 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing