2VIA

Crystal structure of S172AbsSHMT L-Serine external aldimine


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 PH7.5, 0.2MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM L-SER
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.986α = 90
b = 106.283β = 90
c = 57.076γ = 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
11.663091.60.0620.88.94069417.9
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)
11.661.7279.20.265.48.4

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1KL11.6721.4238654204092.70.1790.1780.209RANDOM14.56
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.467
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg12.719
r_dihedral_angle_1_deg5.301
r_scangle_it2.164
r_scbond_it1.379
r_angle_refined_deg1.141
r_mcangle_it0.746
r_mcbond_it0.473
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.467
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg12.719
r_dihedral_angle_1_deg5.301
r_scangle_it2.164
r_scbond_it1.379
r_angle_refined_deg1.141
r_mcangle_it0.746
r_mcbond_it0.473
r_nbtor_refined0.304
r_nbd_refined0.2
r_symmetry_vdw_refined0.169
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.102
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms439
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing