4A01

Crystal Structure of the H-Translocating Pyrophosphatase


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.9769

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 218.619α = 90
b = 88.241β = 125.53
c = 159.105γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B1NSRRCBL13B1

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
12.353098.70.0820.83.841002202
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)
12.352.4398.50.52.73.9

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 DIFFRACTIONMADTHROUGHOUTNONE2.353095106500597.430.169810.168030.20314RANDOM42.995
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]
0.94-3.1-0.86-3.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.697
r_dihedral_angle_4_deg21.578
r_dihedral_angle_3_deg17.068
r_dihedral_angle_1_deg5.439
r_scangle_it4.525
r_scbond_it2.938
r_angle_refined_deg2.056
r_mcangle_it1.7
r_mcbond_it0.948
r_chiral_restr0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.697
r_dihedral_angle_4_deg21.578
r_dihedral_angle_3_deg17.068
r_dihedral_angle_1_deg5.439
r_scangle_it4.525
r_scbond_it2.938
r_angle_refined_deg2.056
r_mcangle_it1.7
r_mcbond_it0.948
r_chiral_restr0.163
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms10862
Nucleic Acid Atoms
Solvent Atoms592
Heterogen Atoms305

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing