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Crystal structure of subunit A mutant P235A/S238C of the A-ATP synthase from pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M4Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 291 50%(v/v) MPD, 0.1M acetate buffer pH 4.5
Crystal Properties Matthews coefficient Solvent content 3.54 65.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.467 α = 90 b = 127.467 β = 90 c = 105.349 γ = 90
Symmetry Space Group P 43 21 2
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 2016-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 2.35 90.13 99.7 0.07 24.07 9.4 36816
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 2.35 2.43 100 0.62 2.83 9.7
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 3M4Y 2.35 30 34785 1830 99.57 0.23707 0.23513 0.2389 0.27239 0.2771 RANDOM 74.719
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] -0.28 -0.28 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.425 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_3_deg 13.586 r_long_range_B_refined 8.441 r_long_range_B_other 8.44 r_dihedral_angle_1_deg 5.714 r_mcangle_it 4.958 r_mcangle_other 4.957 r_scangle_other 4.632 r_mcbond_other 2.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.425 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_3_deg 13.586 r_long_range_B_refined 8.441 r_long_range_B_other 8.44 r_dihedral_angle_1_deg 5.714 r_mcangle_it 4.958 r_mcangle_other 4.957 r_scangle_other 4.632 r_mcbond_other 2.989 r_mcbond_it 2.988 r_scbond_it 2.748 r_scbond_other 2.748 r_angle_refined_deg 1.069 r_angle_other_deg 0.717 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4187 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing