6ZSP

Human serine racemase bound to ATP and malonate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L6B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29325% PEG 3350 230 mM sodium malonate 15 mM magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
1.9737.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.943α = 90
b = 81.191β = 90
c = 134.468γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2018-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.978DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.650.197.50.0690.0790.9999.2476688
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.63810.5770.7050.5121.32.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3L6B1.642.65175542372296.0170.1940.19230.22621.499
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]
-0.5560.5460.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.033
r_dihedral_angle_4_deg20.212
r_dihedral_angle_3_deg13.416
r_dihedral_angle_1_deg6.113
r_lrange_it5.21
r_scangle_it1.927
r_mcangle_it1.689
r_angle_refined_deg1.326
r_scbond_it1.168
r_mcbond_it0.992
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.033
r_dihedral_angle_4_deg20.212
r_dihedral_angle_3_deg13.416
r_dihedral_angle_1_deg6.113
r_lrange_it5.21
r_scangle_it1.927
r_mcangle_it1.689
r_angle_refined_deg1.326
r_scbond_it1.168
r_mcbond_it0.992
r_nbtor_refined0.306
r_nbd_refined0.228
r_xyhbond_nbd_refined0.163
r_symmetry_xyhbond_nbd_refined0.163
r_symmetry_nbd_refined0.152
r_chiral_restr0.095
r_metal_ion_refined0.008
r_gen_planes_refined0.007
r_bond_refined_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4800
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
pointlessdata scaling
MOLREPphasing