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Crystal structure of Russell's viper venom metalloproteinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QUA 1QUA, 2DW0, 1J34 experimental model PDB 2DW0 1QUA, 2DW0, 1J34 experimental model PDB 1J34 1QUA, 2DW0, 1J34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Droplets were prepared by mixing 1l of protein solution and 1l of reservoir solution (0.1M calcium acetate, 0.1M sodium cacodylate, 10% PEG8000, pH 6.5) supplemented with one fifth volume of 10% PEG3350 as an additive and were equilibrated, typically, for one week against 1ml of reservoir solution., VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.16 61.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.35 α = 90 b = 91.73 β = 90 c = 152.93 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 90 CCD ADSC QUANTUM 315 2006-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 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 2.9 50 96.4 0.069 17 6.3 21530 20716
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 2.9 3 79.5 0.212 7 5.5 1293
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 1QUA, 2DW0, 1J34 2.91 44.6 21482 20398 1084 95.9 0.218 0.2223 0.273 0.2696 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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.56 c_angle_deg 1.16 c_improper_angle_d 0.749 c_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5298 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 140
Software Software Software Name Purpose ADSC data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling