1YM5 | pdb_00001ym5

Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	24% PEG 4000, 0.1M sodium acetate pH5, 0.2M ammonium acetate, 30% glycerol, 10mM DDT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.188	α = 90
b = 81.188	β = 90
c = 98.146	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2003-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.04	62.5	98.4			21203	21044	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.043	2.096	92.69

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.05	40	0.4	21044	19923	1081	98.08	0.1908	0.1908	0.18763	0.2	0.25112	0.25	RANDOM	33.236

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]
1.13			1.13		-2.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.745
r_dihedral_angle_3_deg	16.104
r_dihedral_angle_4_deg	14.387
r_dihedral_angle_1_deg	6.876
r_scangle_it	3.308
r_scbond_it	2.399
r_angle_refined_deg	1.667
r_mcangle_it	1.664
r_mcbond_it	1.424
r_angle_other_deg	0.846
r_symmetry_vdw_other	0.257
r_mcbond_other	0.236
r_nbd_refined	0.207
r_nbd_other	0.189
r_symmetry_vdw_refined	0.187
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.182
r_symmetry_hbond_refined	0.179
r_chiral_restr	0.098
r_nbtor_other	0.092
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2292
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing