3NDO

Crystal structure of deoxyribose phosphate aldolase from mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J2W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5290JCSG SCREEN CONDITION H10: 100MM BIS-TRIS PH 5.5, 25% PEG 3350, 200 MM AMMONIUM ACETATE; PROTEIN AT 4.6 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.4349.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.98α = 90
b = 73.2β = 91
c = 64.38γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.9795ALS5.0.2

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
11.2533.4799.80.07314.194.3120211119986-314.38
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)
11.251.281000.5254.38881

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMR, MRTHROUGHOUT1J2W1.2533.47-3120211119884601299.80.1240.1240.1230.144RANDOM7.91
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]
0.19-0.17-0.13-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.638
r_dihedral_angle_4_deg16.428
r_dihedral_angle_3_deg10.465
r_dihedral_angle_1_deg6.117
r_scangle_it5.939
r_scbond_it4.084
r_mcangle_it2.995
r_mcbond_it2.243
r_mcbond_other2.154
r_rigid_bond_restr2.051
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.638
r_dihedral_angle_4_deg16.428
r_dihedral_angle_3_deg10.465
r_dihedral_angle_1_deg6.117
r_scangle_it5.939
r_scbond_it4.084
r_mcangle_it2.995
r_mcbond_it2.243
r_mcbond_other2.154
r_rigid_bond_restr2.051
r_angle_refined_deg1.773
r_angle_other_deg1.09
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3082
Nucleic Acid Atoms
Solvent Atoms543
Heterogen Atoms37

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling