6FHV

Crystal structure of Penicillium oxalicum Glucoamylase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PCB Bis-Tris-propane buffer PEG1500; third Silver bullet condition G2 thiodiglycolic acid, adipic acid, benzoic acid,oxalic acid anhydrous, terephtalic acid, 20 mM Hepes
Crystal Properties
Matthews coefficientSolvent content
3.0860.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 189.253α = 90
b = 189.253β = 90
c = 115.379γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1247.311006.210.353301
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.05

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT24750682261499.920.1890.18740.2193RANDOM36.47
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]
0.050.020.05-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.179
r_dihedral_angle_4_deg18.359
r_dihedral_angle_3_deg15.636
r_dihedral_angle_1_deg6.148
r_angle_other_deg3.837
r_angle_refined_deg1.634
r_mcangle_it1.295
r_mcbond_it0.827
r_mcbond_other0.826
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.179
r_dihedral_angle_4_deg18.359
r_dihedral_angle_3_deg15.636
r_dihedral_angle_1_deg6.148
r_angle_other_deg3.837
r_angle_refined_deg1.634
r_mcangle_it1.295
r_mcbond_it0.827
r_mcbond_other0.826
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_other0.01
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4559
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing