4QQU

Crystal structure of the cobalamin-independent methionine synthase enzyme in a closed conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4L5ZPDB ENTRY 4L5Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429850 mM sodium iodide, 27% w/v PEG3350, 0.25 mM BME, 0.15 mM zinc sulfate, 2 mM homocysteine, 5 mM 5-methyltetrahydrofolate triglutamate, 20 mM Tris-Cl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1943.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.978α = 90
b = 99.102β = 90
c = 103.902γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.97648ALS5.0.3

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
12.9871.711000.1725.47.81641516414
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)
12.983.031000.601

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4L5Z2.9871.71164151554382899.930.180410.175440.2757RANDOM31.671
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]
-1.192.53-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.45
r_dihedral_angle_3_deg16.551
r_dihedral_angle_4_deg14.594
r_dihedral_angle_1_deg6.846
r_long_range_B_refined4.234
r_long_range_B_other4.234
r_mcangle_other2.759
r_scangle_other2.434
r_angle_refined_deg1.635
r_scbond_other1.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.45
r_dihedral_angle_3_deg16.551
r_dihedral_angle_4_deg14.594
r_dihedral_angle_1_deg6.846
r_long_range_B_refined4.234
r_long_range_B_other4.234
r_mcangle_other2.759
r_scangle_other2.434
r_angle_refined_deg1.635
r_scbond_other1.426
r_mcangle_it1.303
r_angle_other_deg0.832
r_mcbond_it0.762
r_mcbond_other0.761
r_scbond_it0.72
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5888
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms69

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling