6AOO

2.15 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HHPPDB entry 3HHP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529520.0 mg/mL protein in 0.3 M sodium chloride, 0.01 M HEPES, pH 7.5, screen: 0.1 M lithium sulfate, 0.1 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 20% w/v PEG3350, 0.25 mM D-Malic acid, cryoprotectant: paratone
Crystal Properties
Matthews coefficientSolvent content
2.0941.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.688α = 90
b = 94.119β = 121.7
c = 73.215γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9MSi(111)2017-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.07822APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rpim I (All)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
12.153097.50.1220.1220.03918.510.933055-334.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.1999.30.7490.7490.2290.8764.311.4

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3HHP2.1529.6831307166097.440.185160.182360.23732RANDOM49.215
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]
5.852.49-3.33-3.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.656
r_dihedral_angle_4_deg10.18
r_dihedral_angle_3_deg8.844
r_long_range_B_refined6.704
r_long_range_B_other6.637
r_scangle_other3.228
r_mcangle_it2.963
r_mcangle_other2.963
r_dihedral_angle_1_deg2.192
r_scbond_it2.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.656
r_dihedral_angle_4_deg10.18
r_dihedral_angle_3_deg8.844
r_long_range_B_refined6.704
r_long_range_B_other6.637
r_scangle_other3.228
r_mcangle_it2.963
r_mcangle_other2.963
r_dihedral_angle_1_deg2.192
r_scbond_it2.014
r_scbond_other2.001
r_mcbond_it1.903
r_mcbond_other1.9
r_angle_refined_deg1.429
r_angle_other_deg0.879
r_chiral_restr0.078
r_gen_planes_refined0.023
r_gen_planes_other0.02
r_bond_refined_d0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4662
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing