3MZO

Crystal structure of a HD-domain phosphohydrolase (lin2634) from LISTERIA INNOCUA at 1.98 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2000M calcium chloride, 28.0000% polyethylene glycol 400, 0.1M HEPES pH 7.5, 0.005M 2'-deoxyadenosine 5'-monophosphate (dAMP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3247.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.243α = 90
b = 121.866β = 121.36
c = 66.621γ = 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 mirror2010-03-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837,0.97939,0.97925SSRLBL9-2

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
11.9848.74199.40.05315.7347810-329.174
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)
1.982.0599.50.5042.7

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 DIFFRACTIONMADTHROUGHOUT1.9848.74147810241899.740.1670.1660.2RANDOM36.888
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]
1.08-0.41-0.86-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.356
r_dihedral_angle_4_deg16.054
r_dihedral_angle_3_deg13.609
r_scangle_it6.413
r_scbond_it4.491
r_dihedral_angle_1_deg4.421
r_mcangle_it2.79
r_mcbond_it1.62
r_angle_refined_deg1.401
r_angle_other_deg0.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.356
r_dihedral_angle_4_deg16.054
r_dihedral_angle_3_deg13.609
r_scangle_it6.413
r_scbond_it4.491
r_dihedral_angle_1_deg4.421
r_mcangle_it2.79
r_mcbond_it1.62
r_angle_refined_deg1.401
r_angle_other_deg0.956
r_mcbond_other0.716
r_chiral_restr0.09
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4965
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms25

Software

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