2VGW

Crystal structure of E53QbsSHMT obtained in the presence of glycine and 5-fomyl tetrahydrofolate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KL1PDB ENTRY 1KL1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.550% MPD, 0.1 M HEPES PH 7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM GLYCINE PROTEIN INCUBATED WITH 2 MM 5-FORMYL TETRAHYDROFOLATE
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.964α = 90
b = 106.46β = 90
c = 56.99γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.865098.80.0517.54.234688925
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)
11.861.93920.383.23.5

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1KL11.8627.0127207302995.20.1720.1680.207RANDOM21.02
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.859
r_dihedral_angle_4_deg15.676
r_dihedral_angle_3_deg13.695
r_dihedral_angle_1_deg5.491
r_scangle_it2.903
r_scbond_it1.906
r_angle_refined_deg1.298
r_mcangle_it1.008
r_mcbond_it0.644
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.859
r_dihedral_angle_4_deg15.676
r_dihedral_angle_3_deg13.695
r_dihedral_angle_1_deg5.491
r_scangle_it2.903
r_scbond_it1.906
r_angle_refined_deg1.298
r_mcangle_it1.008
r_mcbond_it0.644
r_nbtor_refined0.296
r_nbd_refined0.204
r_xyhbond_nbd_refined0.191
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.129
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3117
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling