2W7K | pdb_00002w7k

Crystal structure of Y61AbsSHMT 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
150% MPD, 0.1 M HEPES PH7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM L-SERINE
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.35α = 90
b = 105.23β = 90
c = 56.93γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORSMSINGLE 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
12.43093.60.0818.6331369447.3
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)
12.42.4999.20.424.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1KL12.4223.881300667993.30.2420.240.230.2920.28RANDOM41.75
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]
0.050.08-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.28
r_dihedral_angle_3_deg13.505
r_dihedral_angle_4_deg11.268
r_dihedral_angle_1_deg4.346
r_angle_refined_deg0.873
r_scangle_it0.419
r_nbtor_refined0.29
r_mcangle_it0.251
r_scbond_it0.244
r_nbd_refined0.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.28
r_dihedral_angle_3_deg13.505
r_dihedral_angle_4_deg11.268
r_dihedral_angle_1_deg4.346
r_angle_refined_deg0.873
r_scangle_it0.419
r_nbtor_refined0.29
r_mcangle_it0.251
r_scbond_it0.244
r_nbd_refined0.155
r_mcbond_it0.139
r_symmetry_vdw_refined0.124
r_xyhbond_nbd_refined0.094
r_symmetry_hbond_refined0.09
r_chiral_restr0.055
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 Atoms3109
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing