3VM7

Structure of an Alpha-Amylase from Malbranchea cinnamomea


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62910.2M ammonium acetate, 0.1M sodium acetate trihydrate pH 4.6, 30% w v-1 PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2244.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.9α = 90
b = 84.94β = 105.61
c = 56.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2011-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER1.5418

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
12.2555.521002234466
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)
12.252.3899.90.0650.0650.0781318614

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2549.99223272032520031000.146870.142670.1908RANDOM22.357
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]
-0.17-0.15-0.340.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.346
r_dihedral_angle_3_deg15.505
r_dihedral_angle_4_deg10.916
r_dihedral_angle_1_deg6.334
r_scangle_it2.464
r_scbond_it1.557
r_angle_refined_deg1.419
r_mcangle_it0.957
r_mcbond_it0.485
r_chiral_restr0.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.346
r_dihedral_angle_3_deg15.505
r_dihedral_angle_4_deg10.916
r_dihedral_angle_1_deg6.334
r_scangle_it2.464
r_scbond_it1.557
r_angle_refined_deg1.419
r_mcangle_it0.957
r_mcbond_it0.485
r_chiral_restr0.165
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3660
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms35

Software

Software
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing