2XOK

Refined structure of yeast F1c10 ATPase complex to 3 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HLDPDB ENTRY 2HLD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH80.1 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 coefficientSolvent content
3.8467.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.352α = 90
b = 173.711β = 91.77
c = 137.889γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD1999-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.012074.80.094.11.893955280.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1641.50.183.91.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2HLD3.012091603235274.830.210660.209540.25335RANDOM116.881
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]
4.546.94-6.252.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.576
r_dihedral_angle_3_deg20.207
r_dihedral_angle_4_deg17.071
r_scangle_it6.072
r_dihedral_angle_1_deg6.01
r_scbond_it3.642
r_mcangle_it2.265
r_angle_refined_deg1.368
r_mcbond_it1.197
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.576
r_dihedral_angle_3_deg20.207
r_dihedral_angle_4_deg17.071
r_scangle_it6.072
r_dihedral_angle_1_deg6.01
r_scbond_it3.642
r_mcangle_it2.265
r_angle_refined_deg1.368
r_mcbond_it1.197
r_nbtor_refined0.31
r_nbd_refined0.227
r_symmetry_vdw_refined0.223
r_metal_ion_refined0.197
r_xyhbond_nbd_refined0.15
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 AtomsNumber
Protein Atoms29953
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing