7O5V

Crystal structure of holo-H44A 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	277.15	HEPES, Sodium Citrate

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.914	α = 90
b = 70.914	β = 90
c = 222.572	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 EIGER X 16M		2019-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9766	PETRA III, EMBL c/o DESY	P14 (MX2)

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	1.95	53.77	96.3	0.083	0.116	0.081	0.998	7.3	2.6		29321

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	1.95	2			0.835	1.154	0.794	0.378		2.6

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	1.95	53.769	29316	1484	96.273	0.164	0.1618	0.212	32.704

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]
5.32			5.32		-10.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.652
r_dihedral_angle_4_deg	17.226
r_dihedral_angle_3_deg	14.189
r_dihedral_angle_1_deg	7.251
r_lrange_it	5.475
r_lrange_other	5.46
r_scangle_it	4.129
r_scangle_other	4.129
r_mcangle_it	3.737
r_mcangle_other	3.736
r_scbond_it	3.309
r_scbond_other	3.3
r_mcbond_other	3.144
r_mcbond_it	3.143
r_angle_refined_deg	1.633
r_angle_other_deg	1.327
r_xyhbond_nbd_refined	0.212
r_nbd_other	0.212
r_nbd_refined	0.208
r_symmetry_nbd_other	0.189
r_symmetry_nbd_refined	0.178
r_metal_ion_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.158
r_symmetry_xyhbond_nbd_other	0.123
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.08
r_xyhbond_nbd_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3727
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	13

Software

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