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The structure of superinhibitory phospholamban bound to the calcium pump SERCA1a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C8L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 1 ul of SERCA1a at 15 mg/mL in 2% n-nonyl-beta-D-maltopyranoside (nonyl maltoside) (Anatrace), 20% glycerol, 100 mM MOPS (pH 7.0), 0.12 M sucrose, 80 mM KCl, 3 mM MgCl2, and 2.8 mM EGTA was mixed with 1 uL of phospholamban at 2.1 mg/mL in 20 mM MOPS (pH 7.2), 20% glycerol, and 0.1 % decyl maltoside or 0.01% dodecyl maltoside. This protein mixture was then added to an equal volume of crystallization liquor; 15 % glycerol, 17% (W/V) PEG-2000, 200mM NaOAc, and 5 mM beta-mercoptoethanol), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.73 67.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.591 α = 90 b = 93.094 β = 90 c = 316.375 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 100 CCD ADSC QUANTUM 315 2013-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.98 APS 19-ID
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 2.833 50 97.2 0.084 14.4 5.5 44230 42992 0.2 0.2 88.5
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 2.833 2.89 97.3 0.492 2.6 4.5 2106
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2c8l 2.833 50 0.2 42925 40758 2167 96.68 0.242 0.24139 0.23908 0.28388 0.2966 RANDOM 92.343
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] 1.43 2.36 -3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.324 r_dihedral_angle_4_deg 19.006 r_dihedral_angle_3_deg 18.303 r_dihedral_angle_1_deg 5.678 r_scangle_it 2.013 r_angle_refined_deg 1.196 r_scbond_it 1.172 r_mcangle_it 0.8 r_mcbond_it 0.409 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.324 r_dihedral_angle_4_deg 19.006 r_dihedral_angle_3_deg 18.303 r_dihedral_angle_1_deg 5.678 r_scangle_it 2.013 r_angle_refined_deg 1.196 r_scbond_it 1.172 r_mcangle_it 0.8 r_mcbond_it 0.409 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7861 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 47
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling