3NG3

Crystal structure of deoxyribose phosphate aldolase from mycobacterium avium 104 in a schiff base with an unknown aldehyde


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J2WPDB ENTRY 1J2W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5290JCSG SCREEN CONDITION H3: 100MM BIS-TRIS PH 5.5, 25% PEG 3350; PROTEIN AT 60 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.9157.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.48α = 90
b = 116.32β = 105.76
c = 101.28γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

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
12.1544.7891.30.04323.034.25484850086-327.73
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)
12.152.2195.80.1577.94.064051

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 DIFFRACTIONMR, MRTHROUGHOUTPDB ENTRY 1J2W2.1544.785005225300.1880.1860.228RANDOM21.725
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]
-0.25-0.010.210.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.679
r_dihedral_angle_4_deg17.37
r_dihedral_angle_3_deg11.666
r_dihedral_angle_1_deg6.271
r_scangle_it2.973
r_scbond_it1.859
r_angle_refined_deg1.362
r_mcangle_it1.066
r_angle_other_deg0.909
r_mcbond_it0.619
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.679
r_dihedral_angle_4_deg17.37
r_dihedral_angle_3_deg11.666
r_dihedral_angle_1_deg6.271
r_scangle_it2.973
r_scbond_it1.859
r_angle_refined_deg1.362
r_mcangle_it1.066
r_angle_other_deg0.909
r_mcbond_it0.619
r_mcbond_other0.17
r_chiral_restr0.077
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5948
Nucleic Acid Atoms
Solvent Atoms475
Heterogen Atoms41

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling