6RQA | pdb_00006rqa

Crystal structure of the iminosuccinate reductase of Paracoccus denitrificans in complex with NAD+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OMO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	289	His-tagged iminosuccinate reductase (10 mg/ml) in buffer containing 25 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM MgCl2, 0.1 mM DTT, 5 mM Tb-Xo4, and 5 mM NAD+ was mixed in a ratio of 1:1 with crystallization buffer containing 200 mM Mg(NO3)2 and 20% (w/v) PEG3350 (pH 5.9).

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.386	α = 90
b = 72.407	β = 90
c = 164.266	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 PILATUS 6M-F		2019-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97625	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	2.56	29.4	99.9	0.097	0.105	0.041	0.998	12.6	6.5		20152			46.69

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.56	2.7	100		0.527	0.527	0.573	0.224	1.4	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1OMO	2.56	29.4	1.34	20086	1998	99.92	0.1813	0.1763	0.18	0.225	0.23	52.24

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.9845
f_angle_d	0.5166
f_chiral_restr	0.3198
f_bond_d	0.0036
f_plane_restr	0.0033

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4780
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	120

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHENIX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.