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Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 5.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XTN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 The crystals were grown using in meso crystallization technique
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.1 α = 90 b = 238.98 β = 90 c = 132.48 γ = 90
Symmetry Space Group C 2 2 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 PIXEL PSI PILATUS 6M 2014-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.969 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 47.3 99.3 11 4.2 47136
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) 2.8 2.9 98.6 1.223 1.18 4.1
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 4XTN 2.8 47.3 47136 2482 99.26 0.23257 0.23002 0.2354 0.28016 0.2829 RANDOM 81.276
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] 9.25 -8.69 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.04 r_dihedral_angle_4_deg 13.831 r_long_range_B_refined 12.645 r_long_range_B_other 12.645 r_dihedral_angle_3_deg 12.396 r_scangle_other 9.887 r_mcangle_other 9.559 r_mcangle_it 9.558 r_mcbond_it 6.449 r_mcbond_other 6.442
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.04 r_dihedral_angle_4_deg 13.831 r_long_range_B_refined 12.645 r_long_range_B_other 12.645 r_dihedral_angle_3_deg 12.396 r_scangle_other 9.887 r_mcangle_other 9.559 r_mcangle_it 9.558 r_mcbond_it 6.449 r_mcbond_other 6.442 r_scbond_it 6.44 r_scbond_other 6.44 r_dihedral_angle_1_deg 3.538 r_angle_other_deg 1.059 r_angle_refined_deg 0.603 r_chiral_restr 0.034 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 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 10544 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing