7NNK

Crystal structure of S116A mutant of hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6R62

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292.15	PEG400, HEPES, Magnesium Chloride

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.327	α = 90
b = 71.327	β = 90
c = 223.185	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2020-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.8	74.39	98.5	0.101	0.132	0.085	0.997	8.5	3.4		38705

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)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	99		1.196	1.589	1.037	0.365		3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6R62	1.8	59.533	38701	1936	98.533	0.185	0.1831	0.2247	22.099

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]
-0.165	-0.083		-0.165		0.536

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.644
r_dihedral_angle_4_deg	14.454
r_dihedral_angle_3_deg	12.608
r_dihedral_angle_1_deg	6.954
r_lrange_it	4.351
r_lrange_other	4.185
r_scangle_it	3.139
r_scangle_other	3.138
r_mcangle_it	2.113
r_mcangle_other	2.112
r_scbond_it	2.083
r_scbond_other	2.074
r_angle_refined_deg	1.666
r_mcbond_it	1.529
r_mcbond_other	1.525
r_angle_other_deg	1.343
r_nbd_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.175
r_symmetry_nbd_other	0.146
r_nbtor_refined	0.142
r_xyhbond_nbd_refined	0.14
r_nbd_other	0.122
r_symmetry_nbd_refined	0.116
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.073
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_gen_planes_other	0.005
r_bond_other_d	0.003
r_xyhbond_nbd_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3731
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
Aimless	data scaling
MOLREP	phasing