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Crystal structure of benzamidine-inhibited 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 2AIP PDB entry 2AIP
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 2.12 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.516 α = 90 b = 63.463 β = 99.85 c = 48.216 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 1.54 20.58 99.9 0.084 2.5 35447 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 1.54 1.6 99.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2AIP 1.54 20.58 33670 1774 99.81 0.1763 0.16922 0.16812 0.1679 0.19055 0.1686 RANDOM 17.529
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 35.938 r_dihedral_angle_4_deg 21.094 r_dihedral_angle_3_deg 12.367 r_dihedral_angle_1_deg 6.317 r_scangle_it 2.929 r_scbond_it 1.915 r_angle_refined_deg 1.455 r_mcangle_it 1.278 r_mcbond_it 0.725 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.938 r_dihedral_angle_4_deg 21.094 r_dihedral_angle_3_deg 12.367 r_dihedral_angle_1_deg 6.317 r_scangle_it 2.929 r_scbond_it 1.915 r_angle_refined_deg 1.455 r_mcangle_it 1.278 r_mcbond_it 0.725 r_nbtor_refined 0.323 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.195 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1757 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing