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Crystal structure of the (SR) Calcium ATPase E2-vanadate complex bound to thapsigargin and TNP-AMPPCP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XP5 PDB ENTRY 1XP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 292 19.5% (W/V) PEG2000-MME, 11% (V/V) GLYCEROL, 100 MM MGCL2, 3% (V/V) T-BUTANOL. THE CRYSTALLIZATION DROP WAS EQUILIBRATED AT 19 DEGREES C, AND THE CRYSTAL WAS FLASH FROZEN 13 DAYS AFTER SET-UP., pH 6.8
Crystal Properties Matthews coefficient Solvent content 3.3 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.427 α = 90 b = 118.781 β = 90 c = 141.828 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) PETRA III, EMBL c/o DESY P14 (MX2)
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 3.05 141.8 100 0.12 13 7.3 28547 -3 82.73
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 3.05 3.24 100 0.88 2.3 7.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1XP5 3.05 73.803 1.36 28497 1448 99.92 0.2027 0.1998 0.2076 0.2579 0.2689
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 f_dihedral_angle_d 12.991 f_angle_d 0.797 f_chiral_restr 0.047 f_bond_d 0.011 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7667 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 100
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing