1ZY9

Crystal structure of Alpha-galactosidase (EC 3.2.1.22) (Melibiase) (tm1192) from Thermotoga maritima at 2.34 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP8.32730.2M K3Cirtrate, 20.0% PEG-3350, No Buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
3.463.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.729α = 90
b = 160.533β = 90
c = 88.258γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Flat mirror, Side-defelecting monochromator (Si 111)2005-05-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.979413, 0.918370, 0.979170SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.3442.88980.1290.1295.73.735967
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.4799.40.6030.6031.33.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.3442.50434093179297.410.1650.1620.213RANDOM27.55
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]
0.381.61-1.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.948
r_dihedral_angle_4_deg17.758
r_dihedral_angle_3_deg15.633
r_scangle_it7.69
r_dihedral_angle_1_deg7.102
r_scbond_it5.917
r_mcangle_it3.324
r_mcbond_it2.588
r_angle_refined_deg1.55
r_angle_other_deg0.812
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.948
r_dihedral_angle_4_deg17.758
r_dihedral_angle_3_deg15.633
r_scangle_it7.69
r_dihedral_angle_1_deg7.102
r_scbond_it5.917
r_mcangle_it3.324
r_mcbond_it2.588
r_angle_refined_deg1.55
r_angle_other_deg0.812
r_mcbond_other0.508
r_nbd_refined0.193
r_nbd_other0.184
r_nbtor_refined0.183
r_symmetry_vdw_other0.175
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.137
r_symmetry_vdw_refined0.108
r_chiral_restr0.089
r_nbtor_other0.089
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4232
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
CCP4data scaling
SHELXDphasing
autoSHARPphasing