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Crystal Structure of Proton-Pumping Pyrophosphatase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A01
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 100mM sodium/potassium phosphate (pH 6.2), 200mM NaCl, and 37%(w/v) PEG600
Crystal Properties Matthews coefficient Solvent content 3.99 69.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.703 α = 90 b = 81.637 β = 92.87 c = 264.845 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX300HE 2013-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 30 92.2 0.168 7.5 3.5 54540
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 3.62 85.1 1.175 1.11 3.5
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 MOLECULAR REPLACEMENT THROUGHOUT 4A01 3.5 30 54540 3027 91.11 0.22979 0.2256 0.2282 0.30378 0.3019 RANDOM 119.6
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] 9.45 3.38 0.43 -10.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.435 r_dihedral_angle_3_deg 20.433 r_dihedral_angle_4_deg 19.27 r_long_range_B_refined 14.155 r_long_range_B_other 14.154 r_mcangle_it 9.733 r_mcangle_other 9.733 r_scangle_other 9.307 r_dihedral_angle_1_deg 7.976 r_mcbond_it 6.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.435 r_dihedral_angle_3_deg 20.433 r_dihedral_angle_4_deg 19.27 r_long_range_B_refined 14.155 r_long_range_B_other 14.154 r_mcangle_it 9.733 r_mcangle_other 9.733 r_scangle_other 9.307 r_dihedral_angle_1_deg 7.976 r_mcbond_it 6.002 r_mcbond_other 6.001 r_scbond_it 5.498 r_scbond_other 5.491 r_angle_refined_deg 1.476 r_angle_other_deg 1.055 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21385 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data processing HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction