4RSH

Structure of a putative lipolytic protein of G-D-S-L family from Desulfitobacterium hafniense DCB-2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M Potassium Thiocyanate, 30% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.997α = 90
b = 63.649β = 90
c = 85.647γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDberyllium lenses2014-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.1985.6598.90.19913.613.62933229332-3
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)
12.192.495.60.84311.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.19302779827798148098.720.202690.199140.26994RANDOM23.771
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]
-0.910.660.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.065
r_dihedral_angle_3_deg11.182
r_dihedral_angle_4_deg4.921
r_long_range_B_refined4.708
r_long_range_B_other4.586
r_dihedral_angle_1_deg2.841
r_scangle_other2.163
r_angle_refined_deg1.814
r_scbond_it1.39
r_scbond_other1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.065
r_dihedral_angle_3_deg11.182
r_dihedral_angle_4_deg4.921
r_long_range_B_refined4.708
r_long_range_B_other4.586
r_dihedral_angle_1_deg2.841
r_scangle_other2.163
r_angle_refined_deg1.814
r_scbond_it1.39
r_scbond_other1.39
r_mcangle_it1.363
r_mcangle_other1.362
r_mcbond_it0.902
r_mcbond_other0.902
r_angle_other_deg0.86
r_chiral_restr0.11
r_gen_planes_refined0.024
r_gen_planes_other0.019
r_bond_refined_d0.013
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4116
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms2

Software

Software
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing