2H0V | pdb_00002h0v

Crystal structure of a putative quercetin 2,3-dioxygenase (yxag, bsu39980) from bacillus subtilis at 2.60 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y3T	pdb entry 1y3tA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP		277	10.0% PEG-3350, 0.4M Ammonium Tartrate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
5.31	76.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.416	α = 90
b = 128.659	β = 90
c = 133.889	γ = 90

Symmetry
Space Group	P 21 21 21

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		2005-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

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	2.6	29.778	99.8	0.104	0.104	6.8	5.4		52320			59.22

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	2.6	2.67	100		0.771	0.771	1	4.9

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 1y3tA	2.6	29.78	52271	2666	99.64	0.169	0.167	0.18	0.204	0.2	RANDOM	41.565

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]
5.86			-3.68		-2.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.217
r_dihedral_angle_4_deg	15.409
r_dihedral_angle_3_deg	13.623
r_scangle_it	6.309
r_dihedral_angle_1_deg	6.17
r_scbond_it	4.545
r_mcangle_it	2.609
r_mcbond_it	1.608
r_angle_refined_deg	1.47
r_angle_other_deg	0.808
r_mcbond_other	0.382
r_symmetry_vdw_refined	0.284
r_metal_ion_refined	0.192
r_symmetry_vdw_other	0.192
r_nbd_refined	0.191
r_nbd_other	0.185
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.087
r_nbtor_other	0.086
r_chiral_restr	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5206
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	112

Software

Software
Software Name	Purpose
MolProbity	model building
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing