4CR6

Crystal structure of the N-acetyl-D-mannosamine dehydrogenase without substrates


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D1YPDB ENTRY 2D1Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.1 M HEPES, PH 7.5 AND 30% (W/V) PEG [POLY(ETHYLENE GLYCOL)] 300
Crystal Properties
Matthews coefficientSolvent content
2.2144

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.255α = 81.13
b = 59.062β = 73.29
c = 74.206γ = 79.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray294CCDMARMOSAIC 225 mm CCD2011-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
11.91290.50.066.21.9635792
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)
11.9292.70.173.92

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 2D1Y1.91263579336090.580.209660.208650.22844RANDOM27.924
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]
-0.97-0.43-0.98-0.65-0.072.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.958
r_dihedral_angle_3_deg13.358
r_dihedral_angle_4_deg11.769
r_dihedral_angle_1_deg6.018
r_scangle_it3.226
r_scbond_it1.982
r_angle_refined_deg1.347
r_mcangle_it1.147
r_angle_other_deg1.053
r_mcbond_it0.664
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.958
r_dihedral_angle_3_deg13.358
r_dihedral_angle_4_deg11.769
r_dihedral_angle_1_deg6.018
r_scangle_it3.226
r_scbond_it1.982
r_angle_refined_deg1.347
r_mcangle_it1.147
r_angle_other_deg1.053
r_mcbond_it0.664
r_mcbond_other0.184
r_chiral_restr0.115
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.004
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_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 Atoms7170
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing