5WA0 | pdb_00005wa0

Crystal Structure of the sulfite dehydrogenase, SorT R78Q mutant from Sinorhizobium meliloti

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PW3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	273	0.1 M Bis-Tris propane pH 6.0, 0.2 M sodium malonate, 17.5% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.08	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.52	α = 90
b = 91.78	β = 90.56
c = 109.67	γ = 90

Symmetry
Space Group	P 1 21 1

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 QUANTUM 315r		2013-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	50	86.1	6.3	2.5		95573

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	4PW3	2.1	43.94	79560	4298	74.26	0.2201	0.2173	0.2218	0.2713	0.2716	RANDOM	21.686

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]
-7.74		-2.57	12.31		-4.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.382
r_dihedral_angle_4_deg	16.007
r_dihedral_angle_3_deg	13.551
r_dihedral_angle_1_deg	6.452
r_angle_refined_deg	1.435
r_angle_other_deg	0.938
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10928
Nucleic Acid Atoms
Solvent Atoms	1074
Heterogen Atoms	104

Software

Software
Software Name	Purpose
HKL-2000	data processing
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction