2VN4

Glycoside Hydrolase Family 15 Glucoamylase from Hypocrea jecorina


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GLMPDB ENTRY 1GLM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.525% PEG 3350, 0.20M AMMONIUM ACETATE, 0.10M BIS-TRIS PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.185α = 90
b = 99.232β = 90
c = 121.24γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-5MAX III911-5

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
11.8576.798.30.0920.28.5568583
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)
11.851.9597.70.455.37.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1GLM1.8576.750812272898.090.155590.154190.18211RANDOM22.734
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]
0.380.11-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.184
r_dihedral_angle_4_deg15.149
r_dihedral_angle_3_deg10.617
r_dihedral_angle_1_deg5.216
r_scangle_it2.545
r_scbond_it1.68
r_angle_refined_deg1.204
r_mcangle_it1.171
r_mcbond_it0.641
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.184
r_dihedral_angle_4_deg15.149
r_dihedral_angle_3_deg10.617
r_dihedral_angle_1_deg5.216
r_scangle_it2.545
r_scbond_it1.68
r_angle_refined_deg1.204
r_mcangle_it1.171
r_mcbond_it0.641
r_nbtor_refined0.309
r_nbd_refined0.196
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.127
r_xyhbond_nbd_refined0.111
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4528
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing