6XJM

Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with biuret

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6AZO	PDB ENTRY 6AZO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	1uL 5 mg/mL protein + 1uL 20% w/v PEG3350, 0.2M MgCl2, 20mM Biuret pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.29	α = 90
b = 103.34	β = 90
c = 133.87	γ = 90

Symmetry
Space Group	P 21 21 21

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		2020-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.991840	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.05	81.8	99.7	0.124	8.42	4.25		102760

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.15	99.9		0.425	3.66	4.32

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-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 6AZO	2.05	56.06	54076	2723	99.9	0.184	0.228	21.2

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]
1.012			-1.262		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.061
r_dihedral_angle_4_deg	18.978
r_dihedral_angle_3_deg	14.114
r_dihedral_angle_1_deg	6.801
r_angle_refined_deg	1.64
r_angle_other_deg	1.356
r_nbd_refined	0.204
r_nbd_other	0.172
r_nbtor_refined	0.156
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.081
r_gen_planes_other	0.059
r_gen_planes_refined	0.022
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6856
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building