3GYR

Structure of Phenoxazinone synthase from Streptomyces antibioticus reveals a new type 2 copper center.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5	278	PEG 4000, SODIUM CITRATE, 2- PROPANOL, GLYCEROL, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K, PH 5.00, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.494	α = 117.04
b = 163.456	β = 95.74
c = 164.352	γ = 107.23

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2003-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.3	55.4	86.3	0.082	0.058	11.6	2.4		357511			36.49

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.41	72.4		0.4	0.28	2.6	2.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1GSK	2.3	20	339025	17920	86.34	0.16743	0.16453	0.22237	RANDOM	27.202

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]
-0.15	-0.02	-0.03	0.03	0.15	0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.007
r_dihedral_angle_4_deg	22.079
r_dihedral_angle_3_deg	15.281
r_dihedral_angle_1_deg	8.089
r_scangle_it	3.402
r_mcangle_it	3.034
r_scbond_it	2.402
r_mcbond_it	1.982
r_angle_refined_deg	1.585
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	54720
Nucleic Acid Atoms
Solvent Atoms	4377
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
CrystalClear	data collection
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing