7NR1

Crystal structure of holo-S116A mutant of Hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1

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	PEG 400, HEPES, Magnesium Chloride

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.052	α = 90
b = 71.052	β = 90
c = 222.689	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	2.3	74.23	100	0.189	0.215	0.102	0.995	7.5	8.5		18614

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	2.3	2.38	99.9		1.418	1.706	0.934	0.408		6.1

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	2.3	59.31	18594	910	99.882	0.217	0.2149	0.2512	39.21

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]
-0.303	-0.151		-0.303		0.982

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.717
r_dihedral_angle_4_deg	14.183
r_dihedral_angle_3_deg	12.554
r_dihedral_angle_1_deg	6.41
r_lrange_it	4.059
r_lrange_other	4.058
r_scangle_it	2.62
r_scangle_other	2.618
r_mcangle_it	2.383
r_mcangle_other	2.382
r_scbond_it	1.558
r_scbond_other	1.542
r_mcbond_it	1.485
r_mcbond_other	1.485
r_angle_refined_deg	1.482
r_angle_other_deg	1.109
r_nbd_refined	0.144
r_symmetry_nbd_other	0.126
r_nbtor_refined	0.125
r_nbd_other	0.121
r_xyhbond_nbd_refined	0.088
r_symmetry_nbd_refined	0.072
r_symmetry_nbtor_other	0.069
r_symmetry_xyhbond_nbd_refined	0.069
r_ncsr_local_group_1	0.069
r_chiral_restr	0.059
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3744
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	1

Software

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