2HSZ

Crystal structure of a predicted phosphoglycolate phosphatase (hs_0176) from haemophilus somnus 129pt at 1.90 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.92770.2M NaAcetate, 20.0% PEG-3350, No Buffer pH 7.9, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.9357.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.617α = 90
b = 118.436β = 90
c = 66.503γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2006-05-08MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837,0.97925,1.28281,0.97914SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.89729.9881000.0740.0746.94.851412
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.951000.6530.65313.73744

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 DIFFRACTIONMADTHROUGHOUT1.929.98851362261399.750.1710.1690.205RANDOM21.69
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]
1.18-0.7-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.888
r_dihedral_angle_4_deg14.593
r_dihedral_angle_3_deg12.907
r_scangle_it6.555
r_dihedral_angle_1_deg5.775
r_scbond_it4.61
r_mcangle_it2.831
r_mcbond_it2.09
r_angle_refined_deg1.495
r_angle_other_deg0.948
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.888
r_dihedral_angle_4_deg14.593
r_dihedral_angle_3_deg12.907
r_scangle_it6.555
r_dihedral_angle_1_deg5.775
r_scbond_it4.61
r_mcangle_it2.831
r_mcbond_it2.09
r_angle_refined_deg1.495
r_angle_other_deg0.948
r_mcbond_other0.651
r_symmetry_vdw_other0.256
r_nbd_refined0.246
r_symmetry_hbond_refined0.19
r_nbtor_refined0.186
r_nbd_other0.182
r_xyhbond_nbd_refined0.166
r_symmetry_vdw_refined0.115
r_chiral_restr0.093
r_nbtor_other0.086
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3517
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms30

Software

Software
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
autoSHARPphasing