5H6T

Crystal structure of Hydrazidase from Microbacterium sp. strain HM58-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H0L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2770.1 M imidazole, 0.17 M LiSO4, 2 M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
3.0259.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.162α = 90
b = 128.068β = 90
c = 159.304γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 210r2012-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
11.65099.90.05447.26.1163385
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)
11.61.631000.2328.95.9

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 REPLACEMENTTHROUGHOUT3H0L1.633.97155116819399.680.165510.164850.17809RANDOM14.388
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]
0.010.5-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.308
r_dihedral_angle_4_deg15.321
r_dihedral_angle_3_deg12.285
r_dihedral_angle_1_deg5.795
r_long_range_B_refined3.395
r_long_range_B_other3.336
r_scangle_other2.401
r_scbond_it1.532
r_scbond_other1.532
r_angle_refined_deg1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.308
r_dihedral_angle_4_deg15.321
r_dihedral_angle_3_deg12.285
r_dihedral_angle_1_deg5.795
r_long_range_B_refined3.395
r_long_range_B_other3.336
r_scangle_other2.401
r_scbond_it1.532
r_scbond_other1.532
r_angle_refined_deg1.39
r_mcangle_it1.259
r_mcangle_other1.259
r_angle_other_deg0.971
r_mcbond_it0.78
r_mcbond_other0.779
r_chiral_restr0.083
r_bond_refined_d0.008
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7040
Nucleic Acid Atoms
Solvent Atoms668
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MoRDaphasing