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Refined structure of yeast F1c10 ATPase complex to 3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HLD PDB ENTRY 2HLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 0.1 M TRIS/CL PH8.0, 12% PEG 6000, 150 MM NACL, 1 MM AMP-PNP, 40 MICROM ADP, 1 MM DTT, 0.02% NAN3. MIXED 1:1 WITH PROTEIN SOLUTION UNDER PARAFFIN OIL IN MICROBATCH PLATE.
Crystal Properties Matthews coefficient Solvent content 3.84 67.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.352 α = 90 b = 173.711 β = 91.77 c = 137.889 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 ADSC CCD 1999-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 3.01 20 74.8 0.09 4.1 1.8 93955 2 80.8
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 3.16 41.5 0.18 3.9 1.3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2HLD 3.01 20 91603 2352 74.83 0.21066 0.20954 0.2168 0.25335 RANDOM 116.881
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] 4.54 6.94 -6.25 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.576 r_dihedral_angle_3_deg 20.207 r_dihedral_angle_4_deg 17.071 r_scangle_it 6.072 r_dihedral_angle_1_deg 6.01 r_scbond_it 3.642 r_mcangle_it 2.265 r_angle_refined_deg 1.368 r_mcbond_it 1.197 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.576 r_dihedral_angle_3_deg 20.207 r_dihedral_angle_4_deg 17.071 r_scangle_it 6.072 r_dihedral_angle_1_deg 6.01 r_scbond_it 3.642 r_mcangle_it 2.265 r_angle_refined_deg 1.368 r_mcbond_it 1.197 r_nbtor_refined 0.31 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.223 r_metal_ion_refined 0.197 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other 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_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 29953 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing