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The structure of phospholamban bound to the calcium pump SERCA1a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KYT PDB entry 4KYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 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 % DECYLMALTOSIDE 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)
Crystal Properties Matthews coefficient Solvent content 3.73 67.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.745 α = 90 b = 91.825 β = 90 c = 316.256 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 315r 2013-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.987 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 3.5 50 99 0.087 16.46 4.7 23282 0.2 0.2
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 3.5 3.56 100 0.543 2.47 4.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 4KYT 3.51 48.79 22031 1195 98.91 0.23697 0.23478 0.2312 0.27735 0.2711 RANDOM 135.931
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] 1.54 1.61 -3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.734 r_dihedral_angle_3_deg 18.114 r_dihedral_angle_4_deg 13.558 r_long_range_B_refined 8.479 r_dihedral_angle_1_deg 5.277 r_mcangle_it 4.291 r_scbond_it 2.643 r_mcbond_it 2.509 r_angle_refined_deg 1.021 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.734 r_dihedral_angle_3_deg 18.114 r_dihedral_angle_4_deg 13.558 r_long_range_B_refined 8.479 r_dihedral_angle_1_deg 5.277 r_mcangle_it 4.291 r_scbond_it 2.643 r_mcbond_it 2.509 r_angle_refined_deg 1.021 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7811 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing