7AWV | pdb_00007awv

Azoreductase (AzoRo) from Rhodococcus opacus 1CP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		homology model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	16-20% of isopropanol, 12-16% PEG4000 and 0.1M of sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.652	α = 90
b = 140.652	β = 90
c = 40.568	γ = 120

Symmetry
Space Group	P 62

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 PILATUS3 6M		2019-08-22	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	2.2	70.43	99.87	0.133	0.148	0.063	0.997	10.7	5.6		23710			39.87

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	2.2	2.28	100		1.654	1.84	0.795	0.53		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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	homology model	2.2	70.33	23709	1221	99.903	0.218	0.2161	0.22	0.2611	0.26	53.42

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]
-0.118	-0.059		-0.118		0.382

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.203
r_dihedral_angle_4_deg	18.087
r_dihedral_angle_3_deg	15.853
r_dihedral_angle_1_deg	6.58
r_lrange_it	5.53
r_lrange_other	5.516
r_scangle_it	2.772
r_scangle_other	2.772
r_mcangle_other	2.31
r_mcangle_it	2.309
r_scbond_it	1.746
r_scbond_other	1.746
r_angle_refined_deg	1.731
r_mcbond_it	1.47
r_mcbond_other	1.468
r_angle_other_deg	1.335
r_nbd_refined	0.186
r_symmetry_nbd_refined	0.16
r_nbd_other	0.157
r_symmetry_nbd_other	0.154
r_nbtor_refined	0.149
r_ncsr_local_group_1	0.141
r_symmetry_xyhbond_nbd_refined	0.136
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3119
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	90

Software

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