1WA2 | pdb_00001wa2

Crystal Structure Of H313Q Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase with nitrite bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OE1	PDB ENTRY 1OE1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294	CRYSTALS OF HIS313GLN NIR WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 21OC. 2ML OF 6-8 MG ML-1 PROTEIN IN 10 MM TRIS-HCL PH 7.1 WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONSISTING OF 25% PEG-MME 550, 10 MM ZINC SULPHATE, 0.1M MES PH 6.5 AND SUSPENDED OVER A 500 ML RESERVOIR. CRYSTALS OF BOTH MUTANTS WERE AN INTENSE BLUE COLOUR AND GREW WITHIN TWO DAYS TO APPROXIMATE DIMENSIONS 0.9 X 0.6 X 0.1 MM IN A RHOMBOHEDRAL MORPHOLOGY. FOR HIS313GLN_NO2.-, 10MM SODIUM NITRITE WAS ADDED TO THE RESERVOIR SOLUTION PRIOR TO CRYSTALLISATION.

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.641	α = 90
b = 89.641	β = 90
c = 143.569	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	CCD	ADSC CCD	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1		SRS	PX14.1

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	1.72	60	97.5	0.09	8.7			44676			18.8

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	1.72	1.75	98.4		0.42	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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OE1	1.72	37.53	44676	2257	97.5	0.182	0.18	0.19	0.21	0.2	RANDOM	22.72

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]
0.57	0.28		0.57		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.171
r_scangle_it	2.676
r_scbond_it	1.718
r_angle_refined_deg	1.444
r_mcangle_it	1.128
r_angle_other_deg	0.945
r_mcbond_it	0.653
r_symmetry_vdw_other	0.294
r_nbd_other	0.253
r_nbd_refined	0.234
r_symmetry_hbond_refined	0.195
r_xyhbond_nbd_refined	0.17
r_symmetry_vdw_refined	0.155
r_chiral_restr	0.085
r_nbtor_other	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2523
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing