3R19 | pdb_00003r19

Chicken sulfite oxidase triple mutant with altered activity and substrate affinity

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A99	PDB ENTRY 2A99

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	15 % PEG 6000 (W/V), 5 % MPD (V/V), 100 mM MES pH 6.5, and 2% (w/v) benzamidine hydrochloride hydrate, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.599	α = 90
b = 85.599	β = 90
c = 152.798	γ = 90

Symmetry
Space Group	I 41

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	MARMOSAIC 225 mm CCD		2008-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	47.46	99.7	0.103	39.6	6.6	31937	31937	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	97.2		0.288	4.3	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2A99	2.1	47.46	2	30282	30282	1610	99.5	0.237	0.169	0.167	0.18	0.19	0.2	RANDOM	38.777

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]
1.18			1.18		-2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.556
r_dihedral_angle_4_deg	20.131
r_dihedral_angle_3_deg	12.612
r_dihedral_angle_1_deg	5.868
r_scangle_it	2.429
r_scbond_it	1.469
r_angle_refined_deg	1.188
r_mcangle_it	0.842
r_mcbond_it	0.44
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.556
r_dihedral_angle_4_deg	20.131
r_dihedral_angle_3_deg	12.612
r_dihedral_angle_1_deg	5.868
r_scangle_it	2.429
r_scbond_it	1.469
r_angle_refined_deg	1.188
r_mcangle_it	0.842
r_mcbond_it	0.44
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2865
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	25

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.