3GIW

CRYSTAL STRUCTURE OF a DUF574 family protein (SAV_2177) FROM STREPTOMYCES AVERMITILIS MA-4680 AT 1.45 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52931.0 M Na citrate, 0.1 M Sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3647.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.716α = 90
b = 49.669β = 94.72
c = 45.132γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-01-08MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837, 0.97927SSRLBL9-2

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
11.4527.18694.80.03613.44.06350240-315.987
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)
11.451.585.90.3332.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.4527.18650239255198.990.1570.1560.176RANDOM18.557
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]
-0.35-0.42-0.81.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg14.108
r_dihedral_angle_3_deg11.96
r_dihedral_angle_1_deg5.86
r_scangle_it2.498
r_mcangle_it1.815
r_scbond_it1.719
r_angle_refined_deg1.511
r_mcbond_it1.249
r_angle_other_deg1.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg14.108
r_dihedral_angle_3_deg11.96
r_dihedral_angle_1_deg5.86
r_scangle_it2.498
r_mcangle_it1.815
r_scbond_it1.719
r_angle_refined_deg1.511
r_mcbond_it1.249
r_angle_other_deg1.003
r_mcbond_other0.307
r_symmetry_vdw_other0.286
r_nbd_refined0.219
r_nbd_other0.203
r_symmetry_hbond_refined0.198
r_nbtor_refined0.174
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.169
r_xyhbond_nbd_other0.102
r_chiral_restr0.099
r_nbtor_other0.081
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2023
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing