7NUJ

Crystal structure of holo-SwHPA-Mg (hydroxy ketone aldolase) 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
1.87	34.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.102	α = 90
b = 71.102	β = 90
c = 223.196	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		2019-03-03	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	1.9	59.36	99.9	0.108	0.135	0.08	0.998	9.5	5.3		33131

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	1.9	1.94			1.137	1.413	0.823	0.562		5.3

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	1.9	59.359	33130	1574	99.876	0.167	0.1648	0.2044	25.889

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]
-1.021	-0.51		-1.021		3.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.068
r_dihedral_angle_4_deg	16.363
r_dihedral_angle_3_deg	11.754
r_dihedral_angle_1_deg	6.631
r_lrange_it	5.075
r_lrange_other	4.928
r_scangle_it	3.795
r_scangle_other	3.795
r_scbond_it	2.5
r_scbond_other	2.496
r_mcangle_it	2.32
r_mcangle_other	2.319
r_mcbond_it	1.665
r_mcbond_other	1.664
r_angle_refined_deg	1.566
r_angle_other_deg	1.309
r_nbd_refined	0.194
r_symmetry_nbd_refined	0.192
r_xyhbond_nbd_refined	0.149
r_symmetry_nbd_other	0.145
r_nbtor_refined	0.138
r_nbd_other	0.123
r_symmetry_xyhbond_nbd_refined	0.113
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.072
r_ncsr_local_group_1	0.065
r_symmetry_metal_ion_refined	0.018
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3747
Nucleic Acid Atoms
Solvent Atoms	407
Heterogen Atoms	2

Software

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