3GVI

Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5290JCSG+ SCREEN, H3: 25% PEG 3350, 100MM BISTRIS, BRABA.00005.A AT 28.5MG/ML, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.6253.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.39α = 90
b = 193.9β = 90
c = 102.68γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

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
12.25193.997.30.05118.824.210235099622-328.89
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)
2.252.3183.70.1525.627486

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUTpdb entry 3GVH2.251939961799617500097.30.1770.1740.228RANDOM14.95
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]
0.490.67-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.254
r_dihedral_angle_4_deg14.413
r_dihedral_angle_3_deg14.105
r_dihedral_angle_1_deg5.58
r_scangle_it3.748
r_scbond_it2.34
r_angle_refined_deg1.525
r_mcangle_it1.412
r_angle_other_deg0.927
r_mcbond_it0.756
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.254
r_dihedral_angle_4_deg14.413
r_dihedral_angle_3_deg14.105
r_dihedral_angle_1_deg5.58
r_scangle_it3.748
r_scbond_it2.34
r_angle_refined_deg1.525
r_mcangle_it1.412
r_angle_other_deg0.927
r_mcbond_it0.756
r_mcbond_other0.232
r_chiral_restr0.086
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms13710
Nucleic Acid Atoms
Solvent Atoms1311
Heterogen Atoms162

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling