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Crystal structure of an ATP synthase subunit beta 1 (F1-B1) from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 ButhA.17369.c.A1.PW35952 at 19.9 mg/mL with 1 mM MnCl2 and 1 mM ATPgS against PACT screen condition B5, 0.1 M MIB buffer pH 8.0, 25% PEG 1500 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 242856b5, unique tracking ID ppm0-6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.68 54.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.42 α = 90 b = 97.99 β = 90 c = 127.54 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 300 mm CCD 2014-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.2 50 99.9 0.045 22.69 6 29798 29756 -3 50.869
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 2.2 2.26 99.9 0.541 3.49
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 3oaa 2.2 50 29696 1462 99.87 0.1959 0.1939 0.2009 0.2361 0.2329 RANDOM 56.812
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] 2.96 -0.52 -2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.803 r_dihedral_angle_4_deg 17.391 r_dihedral_angle_3_deg 14.013 r_dihedral_angle_1_deg 5.802 r_mcangle_it 3.668 r_mcbond_it 2.418 r_mcbond_other 2.417 r_angle_refined_deg 1.465 r_angle_other_deg 0.804 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.803 r_dihedral_angle_4_deg 17.391 r_dihedral_angle_3_deg 14.013 r_dihedral_angle_1_deg 5.802 r_mcangle_it 3.668 r_mcbond_it 2.418 r_mcbond_other 2.417 r_angle_refined_deg 1.465 r_angle_other_deg 0.804 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3201 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction BALBES phasing