2VI9

Crystal structure of S172AbsSHMT Glycine 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, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM GLY
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.075α = 90
b = 105.953β = 90
c = 56.89γ = 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
123098.80.113.34.32528527.5
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)
122.0798.80.52.84.3

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 1KL1224.0123992129098.60.1970.1950.245RANDOM26.07
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.452
r_dihedral_angle_4_deg13.436
r_dihedral_angle_3_deg12.765
r_dihedral_angle_1_deg4.945
r_scangle_it1.186
r_angle_refined_deg0.986
r_scbond_it0.724
r_mcangle_it0.46
r_nbtor_refined0.295
r_mcbond_it0.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.452
r_dihedral_angle_4_deg13.436
r_dihedral_angle_3_deg12.765
r_dihedral_angle_1_deg4.945
r_scangle_it1.186
r_angle_refined_deg0.986
r_scbond_it0.724
r_mcangle_it0.46
r_nbtor_refined0.295
r_mcbond_it0.288
r_nbd_refined0.177
r_symmetry_vdw_refined0.139
r_symmetry_hbond_refined0.106
r_xyhbond_nbd_refined0.1
r_chiral_restr0.066
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms202
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing