3OC6

Crystal structure of 6-phosphogluconolactonase from mycobacterium smegmatis, apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ICO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2289JCSG CONDITION C1: 0.1 M PHOSPHATE-CITRATE PH 4.2, 20% PEG 8000, 200 MM NACL, PROTEIN (MYSMA.01244.A.A1.PW28797) AT 29 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties
Matthews coefficientSolvent content
2.8857.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.44α = 90
b = 176.44β = 90
c = 38.37γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.00ALS5.0.2

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
12.144.111000.10123.9914.31811818113-328.48
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)
12.12.151000.5395.714.41324

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3ICO2.144.1118118180419220.1530.1530.1520.184RANDOM23.32
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.789
r_dihedral_angle_4_deg17.904
r_dihedral_angle_3_deg13.307
r_dihedral_angle_1_deg5.963
r_scangle_it4.077
r_scbond_it2.46
r_angle_refined_deg1.505
r_mcangle_it1.477
r_angle_other_deg0.907
r_mcbond_it0.833
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.789
r_dihedral_angle_4_deg17.904
r_dihedral_angle_3_deg13.307
r_dihedral_angle_1_deg5.963
r_scangle_it4.077
r_scbond_it2.46
r_angle_refined_deg1.505
r_mcangle_it1.477
r_angle_other_deg0.907
r_mcbond_it0.833
r_mcbond_other0.231
r_chiral_restr0.086
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 Atoms1787
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling