7O5W

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


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
1.9135.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.996α = 90
b = 70.996β = 90
c = 222.817γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97620PETRA 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
11.274.271000.0780.0870.0390.99915.59.7130983
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)
11.21.220.4780.5390.2470.9069.5

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 REPLACEMENTFREE R-VALUE6R621.253.889130980660499.9870.120.11850.146311.71
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]
-0.091-0.046-0.0910.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.328
r_dihedral_angle_4_deg17.052
r_dihedral_angle_3_deg11.691
r_dihedral_angle_1_deg5.915
r_rigid_bond_restr4.075
r_lrange_it2.493
r_scangle_it2.398
r_scangle_other2.398
r_scbond_it2.152
r_scbond_other2.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.328
r_dihedral_angle_4_deg17.052
r_dihedral_angle_3_deg11.691
r_dihedral_angle_1_deg5.915
r_rigid_bond_restr4.075
r_lrange_it2.493
r_scangle_it2.398
r_scangle_other2.398
r_scbond_it2.152
r_scbond_other2.132
r_lrange_other2.12
r_angle_refined_deg2.019
r_angle_other_deg1.669
r_mcangle_other1.321
r_mcangle_it1.32
r_mcbond_it1.122
r_mcbond_other1.12
r_symmetry_xyhbond_nbd_other0.473
r_symmetry_nbd_refined0.307
r_symmetry_xyhbond_nbd_refined0.265
r_nbd_other0.262
r_xyhbond_nbd_refined0.234
r_nbd_refined0.227
r_symmetry_nbd_other0.179
r_nbtor_refined0.179
r_chiral_restr0.127
r_ncsr_local_group_10.091
r_symmetry_nbtor_other0.09
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3753
Nucleic Acid Atoms
Solvent Atoms605
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing