7O9R

Crystal structure of holo-H44A 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	277.15	HEPES, Sodium Citrate

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.881	α = 90
b = 70.881	β = 90
c = 223.18	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		2019-04-26	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	1.85	59.19	94	0.153	0.18	0.094	0.996	4.6	3.8		33572

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	1.85	1.89			1.537	1.801	0.916	0.602		3.7

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	1.85	59.19	33393	1714	93.417	0.16	0.158	0.1959	27.832

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]
0.054	0.027		0.054		-0.177

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.695
r_dihedral_angle_4_deg	17.75
r_dihedral_angle_3_deg	12.895
r_dihedral_angle_1_deg	6.614
r_lrange_it	5.31
r_lrange_other	5.253
r_scangle_it	3.876
r_scangle_other	3.875
r_mcangle_it	2.687
r_mcangle_other	2.686
r_scbond_it	2.56
r_scbond_other	2.56
r_mcbond_it	1.885
r_mcbond_other	1.884
r_angle_refined_deg	1.443
r_angle_other_deg	1.342
r_symmetry_metal_ion_refined	0.405
r_symmetry_nbd_refined	0.322
r_metal_ion_refined	0.23
r_nbd_refined	0.214
r_nbd_other	0.196
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.027
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3736
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	15

Software

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