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Structure of the (SR) Ca2+-ATPase bound to a Tetrahydrocarbazole and TNP-ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AGV 2AGV (individual domains)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 glycerol, PEG6000, Na acetate pH 7.2, MPD, beta-OG
Crystal Properties Matthews coefficient Solvent content 3.67 66.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.62 α = 90 b = 224.63 β = 90 c = 57.05 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 2M 2012-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 56.16 99.4 0.099 0.99 15.1 20 61971 72.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.3 97.7 0.78 2.2
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 (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 FREE R-VALUE 2AGV (individual domains) 3 56.158 1.29 61945 3074 99.32 0.2156 0.2129 0.2191 0.2666 0.2664 Random selection
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 14.987 f_angle_d 0.63 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7596 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 158
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing