3MNF

Crystal structure of PAC2 family protein from Streptomyces avermitilis MA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62971.0M Na/K tartrate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
4.4372.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.943α = 90
b = 143.943β = 90
c = 81.121γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929APS19-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
12.975099.70.10641.512.61104110559-376.6
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)
33.051000.8474.8413.1507

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 DIFFRACTIONSADTHROUGHOUT2.9750104841048450299.120.216960.216960.215720.24108RANDOM88.778
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]
-0.74-0.37-0.741.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.35
r_dihedral_angle_4_deg18.461
r_dihedral_angle_3_deg17.272
r_dihedral_angle_1_deg6.485
r_scangle_it2.716
r_scbond_it1.557
r_angle_refined_deg1.511
r_mcangle_it1.046
r_mcbond_it0.54
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.35
r_dihedral_angle_4_deg18.461
r_dihedral_angle_3_deg17.272
r_dihedral_angle_1_deg6.485
r_scangle_it2.716
r_scbond_it1.557
r_angle_refined_deg1.511
r_mcangle_it1.046
r_mcbond_it0.54
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1747
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms1

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing