2W7H

Crystal structure of Y51FbsSHMT obtained in the presence of Gly and 5- Formyl Tetrahydrofolate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
150% MPD, 0.1 M HEPES PH 7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM GLY, 2 MM 5-FORMYL TETRAHYDROFOLATE
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.051α = 90
b = 106.473β = 90
c = 57.181γ = 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
11.663092.20.0626.220.34113823.6
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)
11.661.7281.40.463.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1KL11.6721.339060206793.20.1860.1840.215RANDOM20.44
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]
-0.050.040.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.328
r_dihedral_angle_4_deg15.489
r_dihedral_angle_3_deg12.508
r_dihedral_angle_1_deg5.368
r_scangle_it2.723
r_scbond_it1.73
r_angle_refined_deg1.242
r_mcangle_it0.913
r_mcbond_it0.572
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.328
r_dihedral_angle_4_deg15.489
r_dihedral_angle_3_deg12.508
r_dihedral_angle_1_deg5.368
r_scangle_it2.723
r_scbond_it1.73
r_angle_refined_deg1.242
r_mcangle_it0.913
r_mcbond_it0.572
r_nbtor_refined0.302
r_nbd_refined0.202
r_symmetry_vdw_refined0.167
r_symmetry_hbond_refined0.133
r_xyhbond_nbd_refined0.107
r_chiral_restr0.083
r_bond_refined_d0.01
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 Atoms3115
Nucleic Acid Atoms
Solvent Atoms434
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing