3B85

Crystal structure of predicted phosphate starvation-induced ATPase PhoH2 from Corynebacterium glutamicum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52911.26M Ammonium sulfate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2444.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.668α = 90
b = 98.668β = 90
c = 36.675γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97924APS19-ID

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
12.355093.90.0987.65.41569315693-350.1
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)
12.352.472.80.4481.83.4814

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.3536.69156251562578993.910.1830.1830.180.234RANDOM48.745
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]
-1.73-0.86-1.732.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.309
r_dihedral_angle_4_deg21.27
r_dihedral_angle_3_deg18.164
r_dihedral_angle_1_deg6.301
r_scangle_it3.42
r_scbond_it2.406
r_angle_refined_deg1.569
r_mcangle_it1.503
r_mcbond_it1.209
r_angle_other_deg0.949
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.309
r_dihedral_angle_4_deg21.27
r_dihedral_angle_3_deg18.164
r_dihedral_angle_1_deg6.301
r_scangle_it3.42
r_scbond_it2.406
r_angle_refined_deg1.569
r_mcangle_it1.503
r_mcbond_it1.209
r_angle_other_deg0.949
r_symmetry_vdw_other0.251
r_nbd_other0.203
r_nbd_refined0.201
r_mcbond_other0.175
r_nbtor_refined0.171
r_symmetry_vdw_refined0.164
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.147
r_nbtor_other0.089
r_chiral_restr0.087
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.003
r_xyhbond_nbd_other0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2884
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms45

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building