8XND | pdb_00008xnd

Crystal structure of serine hydroxymethyltransferase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BJ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M Sodium HEPES pH 7.5,30 %(v/v) PEG 300

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.54α = 90
b = 151.54β = 90
c = 234.97γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-08-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.18057CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
13.4548.5399.90.1610.99510.45.379382
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.453.520.787

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT3.4548.5375288404999.920.154990.1530.14310.192050.1711RANDOM90.799
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]
46.3846.38-92.77
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined27.293
r_mcangle_it21.374
r_dihedral_angle_3_deg18.804
r_scbond_it17.256
r_mcbond_it15.343
r_dihedral_angle_2_deg15.204
r_dihedral_angle_1_deg6.628
r_angle_refined_deg2.693
r_chiral_restr0.167
r_bond_refined_d0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined27.293
r_mcangle_it21.374
r_dihedral_angle_3_deg18.804
r_scbond_it17.256
r_mcbond_it15.343
r_dihedral_angle_2_deg15.204
r_dihedral_angle_1_deg6.628
r_angle_refined_deg2.693
r_chiral_restr0.167
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_it
r_scangle_other
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 Atoms14528
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing