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The UDP complex structure of the sixth gene product of the F1-ATPase operon of Rhodobacter blasticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NXV PDB entry 2NXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 100mM sodium citrate (pH6.0) and 75mM magnesium acetate. Mixed 4+4ul with protein sample, hanging drop, vapor diffusion, temperature 298K., VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.36 63.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.37 α = 90 b = 89.928 β = 90 c = 69.572 γ = 90
Symmetry Space Group P 21 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 MAR CCD 165 mm 2006-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.043 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.65 20 99.9 0.071 16.7 6.1 93646 18.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 100 0.388 4.6 6.1 13554
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 PDB entry 2NXV 1.65 12.99 93484 4687 99.97 0.16 0.159 0.1564 0.184 0.1832 RANDOM 19.201
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.493 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_3_deg 11.838 r_dihedral_angle_1_deg 6.054 r_scangle_it 5.306 r_scbond_it 3.483 r_mcangle_it 2.15 r_angle_refined_deg 2.104 r_mcbond_it 1.514 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.493 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_3_deg 11.838 r_dihedral_angle_1_deg 6.054 r_scangle_it 5.306 r_scbond_it 3.483 r_mcangle_it 2.15 r_angle_refined_deg 2.104 r_mcbond_it 1.514 r_nbtor_refined 0.311 r_chiral_restr 0.274 r_symmetry_vdw_refined 0.24 r_symmetry_hbond_refined 0.218 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.151 r_bond_refined_d 0.026 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4040 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 27
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing