5VFB

1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas aeruginosa in Complex with Glycolic Acid.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5295Protein: 14.6 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (A7), 0.2M Sodium chloride, 0.1M Sodium acetate pH (5.0), 20% (w/v) PEG 6000.
Crystal Properties
Matthew coefficientSolvent content
2.0640.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.385α = 90
b = 111.712β = 100.42
c = 96.954γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-03-28MSINGLE 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)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
11.363099.10.0870.0870.04715.44.3280381-310.5
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)
11.361.3896.50.7150.7150.4260.6072.073.7

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 REPLACEMENTTHROUGHOUT3S9Z1.3629.622663961394498.930.144530.143330.16782RANDOM11.977
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]
0.02-0.13-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.676
r_dihedral_angle_4_deg13.994
r_dihedral_angle_3_deg9.905
r_long_range_B_refined4.605
r_long_range_B_other3.997
r_dihedral_angle_1_deg3.926
r_scangle_other1.773
r_angle_refined_deg1.446
r_scbond_it1.149
r_scbond_other1.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.676
r_dihedral_angle_4_deg13.994
r_dihedral_angle_3_deg9.905
r_long_range_B_refined4.605
r_long_range_B_other3.997
r_dihedral_angle_1_deg3.926
r_scangle_other1.773
r_angle_refined_deg1.446
r_scbond_it1.149
r_scbond_other1.149
r_mcangle_it1.094
r_mcangle_other1.094
r_angle_other_deg0.867
r_mcbond_it0.664
r_mcbond_other0.664
r_chiral_restr0.093
r_gen_planes_refined0.024
r_gen_planes_other0.021
r_bond_refined_d0.009
r_bond_other_d0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11050
Nucleic Acid Atoms
Solvent Atoms2247
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing