3LWD

Crystal structure of Putative 6-phosphogluconolactonase (YP_574786.1) from Chromohalobacter salexigens DSM 3043 at 1.88 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527710.0000% iso-Propanol, 20.0000% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.9257.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.647α = 90
b = 60.647β = 90
c = 133.089γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2009-12-03MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97937,0.97898SSRLBL11-1

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
11.7548.8496.30.04514.4965927-3
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)
11.751.9587.80.4642.4

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 DIFFRACTIONMADTHROUGHOUT1.7548.8627822148899.770.159650.158280.18628RANDOM11.63
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]
1.640.821.64-2.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.058
r_dihedral_angle_4_deg18.824
r_dihedral_angle_3_deg12.63
r_dihedral_angle_1_deg4.445
r_scangle_it3.195
r_scbond_it1.968
r_mcangle_it1.183
r_angle_refined_deg1.154
r_angle_other_deg0.777
r_mcbond_it0.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.058
r_dihedral_angle_4_deg18.824
r_dihedral_angle_3_deg12.63
r_dihedral_angle_1_deg4.445
r_scangle_it3.195
r_scbond_it1.968
r_mcangle_it1.183
r_angle_refined_deg1.154
r_angle_other_deg0.777
r_mcbond_it0.658
r_mcbond_other0.206
r_chiral_restr0.083
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1669
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms13

Software

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