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Crystal structure of Thermotoga Maritima sodium pumping membrane integral pyrophosphatase with metal ions in active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other OUR BACKBONE HELICAL LOW RESOLUTION MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 19-22% PEG 350, 0.1 M MES-NAOH PH 6.5, 0.2 M CA2CL, 2 MM DTT
Crystal Properties Matthews coefficient Solvent content 2.96 58.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.52 α = 90 b = 107.779 β = 108.5 c = 102.521 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD RH-COATED SI MIRROR AND RH- COATED TOROIDAL SI MIRROR 2012-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
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 2.6 50 97.8 0.05 22.7 7.43 49279 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 2.6 2.76 95.1 0.84 2.14 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT OUR BACKBONE HELICAL LOW RESOLUTION MODEL 2.6 50 49279 2622 97.76 0.20658 0.20458 0.24478 0.2531 RANDOM 71.691
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] -6.51 1.57 -0.08 7.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.917 r_dihedral_angle_3_deg 19.878 r_dihedral_angle_4_deg 16.994 r_dihedral_angle_1_deg 6.356 r_angle_refined_deg 1.703 r_angle_other_deg 1.281 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.917 r_dihedral_angle_3_deg 19.878 r_dihedral_angle_4_deg 16.994 r_dihedral_angle_1_deg 6.356 r_angle_refined_deg 1.703 r_angle_other_deg 1.281 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 9965 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC model building XDS data reduction XDS data scaling SHELXCD phasing SHELXD phasing SHARP phasing REFMAC phasing PHENIX phasing