7O87

Crystal structure of holo-F210W mutant of Hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6R62 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277.15HEPES, Sodium Citrate
Crystal Properties
Matthews coefficientSolvent content
1.935.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.814α = 90
b = 70.814β = 90
c = 221.899γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.573.9798.20.1110.1480.0980.9963.365270
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5399.10.9571.2780.840.3753.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6R621.553.73165265327298.1580.1860.18390.225416.909
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]
-0.096-0.048-0.0960.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.407
r_dihedral_angle_4_deg20.695
r_dihedral_angle_3_deg12.746
r_dihedral_angle_1_deg6.59
r_lrange_it4.09
r_lrange_other4.024
r_scangle_it3.05
r_scangle_other3.05
r_scbond_it2.039
r_scbond_other2.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.407
r_dihedral_angle_4_deg20.695
r_dihedral_angle_3_deg12.746
r_dihedral_angle_1_deg6.59
r_lrange_it4.09
r_lrange_other4.024
r_scangle_it3.05
r_scangle_other3.05
r_scbond_it2.039
r_scbond_other2.005
r_mcangle_it1.955
r_mcangle_other1.955
r_angle_refined_deg1.582
r_angle_other_deg1.428
r_mcbond_it1.337
r_mcbond_other1.335
r_symmetry_metal_ion_refined0.587
r_symmetry_nbd_refined0.448
r_nbd_refined0.21
r_nbd_other0.196
r_symmetry_nbd_other0.177
r_xyhbond_nbd_refined0.176
r_nbtor_refined0.159
r_symmetry_xyhbond_nbd_refined0.158
r_chiral_restr0.08
r_symmetry_nbtor_other0.08
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3753
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing