4AJ1 | pdb_00004aj1

rat LDHA in complex with N-(2-(methylamino)-1,3-benzothiazol-6-yl) acetamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherINTERNAL RAT LDHA STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
171.5 M NA MALONATE PH 7.0, 2% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.241α = 90
b = 81.914β = 96.18
c = 128.869γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944VARIMAXHF2008-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
11.8764.0673.80.078.32.81785482
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)
11.871.9433.70.272.21.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTINTERNAL RAT LDHA STRUCTURE1.8749.3774127386073.310.176290.173490.180.231090.24RANDOM22.782
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]
-0.030.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.243
r_dihedral_angle_4_deg18.616
r_dihedral_angle_3_deg13.611
r_dihedral_angle_1_deg6.322
r_angle_refined_deg1.482
r_angle_other_deg0.951
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10025
Nucleic Acid Atoms
Solvent Atoms1025
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing