4I1I

Crystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin in complex with NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H7PPDB ENTRY 4H7P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6290EmeraldBio PACT screen a3: 25% PEG 1500, 100mM SPG buffer pH 6.0; LemaA.01212.a.A1.P001468 at 15mg/ml + 2.5mM NAD, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.141.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.82α = 90
b = 65.13β = 110.67
c = 77.49γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.55099.20.05912.273.79675095941-325.149
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)
11.51.5494.20.350.352.782.67124

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4H7P1.548.59675095920479499.260.14590.14590.14490.1655RANDOM21.1806
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]
0.090.070.1-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.382
r_dihedral_angle_4_deg14.204
r_dihedral_angle_3_deg11.232
r_dihedral_angle_1_deg6.367
r_mcangle_it1.84
r_angle_refined_deg1.664
r_mcbond_it1.189
r_mcbond_other1.189
r_angle_other_deg0.803
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.382
r_dihedral_angle_4_deg14.204
r_dihedral_angle_3_deg11.232
r_dihedral_angle_1_deg6.367
r_mcangle_it1.84
r_angle_refined_deg1.664
r_mcbond_it1.189
r_mcbond_other1.189
r_angle_other_deg0.803
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4567
Nucleic Acid Atoms
Solvent Atoms623
Heterogen Atoms79

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing