7O5R

Crystal structure of holo-SwHPA-Mn (hydroxyketoacid aldolase) from Sphingomonas wittichii RW1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		apo-SwHKA

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
2.07	40.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.54	α = 90
b = 71.54	β = 90
c = 225.394	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		2018-12-10	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	1.65	75.131	99.9	0.15	0.184	0.106	0.99	9.1	5.9		51766

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	1.65	1.68	100		0.997	1.222	0.69	0.325		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	apo-SwHKA	1.65	75.131	51761	2506	99.929	0.161	0.1596	0.1931	11.952

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]
-0.316			-0.316		0.633

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.423
r_dihedral_angle_3_deg	14.629
r_dihedral_angle_2_deg	9.267
r_dihedral_angle_1_deg	6.135
r_lrange_it	4.763
r_lrange_other	4.511
r_scangle_it	2.789
r_scangle_other	2.788
r_mcangle_other	1.918
r_mcangle_it	1.916
r_scbond_it	1.906
r_scbond_other	1.876
r_angle_refined_deg	1.869
r_mcbond_it	1.328
r_mcbond_other	1.32
r_angle_other_deg	0.631
r_symmetry_nbd_refined	0.34
r_symmetry_metal_ion_refined	0.254
r_nbd_refined	0.238
r_xyhbond_nbd_refined	0.229
r_symmetry_xyhbond_nbd_refined	0.227
r_metal_ion_refined	0.195
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.175
r_nbd_other	0.163
r_symmetry_xyhbond_nbd_other	0.154
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3754
Nucleic Acid Atoms
Solvent Atoms	464
Heterogen Atoms	7

Software

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