4P9G | pdb_00004p9g

Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EBR	3ebr, 2oq1, 3bal, 3cjx
experimental model	PDB	2OQ1	3ebr, 2oq1, 3bal, 3cjx
experimental model	PDB	3BAL	3ebr, 2oq1, 3bal, 3cjx
experimental model	PDB	3CJX	3ebr, 2oq1, 3bal, 3cjx

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	Protein solution: protein concentration = 5 mg/ml in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM beta-mercaptoethanol. Chymotrypsin was added in a 1:50 mass-ratio prior to setting up hanging-drop crystallisation trials. Well solution: 10 % w/v PEG 1k and 10 % PEG 10k (Molecular Dimensions Structure Screen 2, condition 46).

Crystal Properties
Matthews coefficient	Solvent content
2.48	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.557	α = 90
b = 82.557	β = 90
c = 114.008	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	MAR CCD 165 mm		2013-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	1.072	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	57	86.3	0.136	12.6	9.8		10549

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.3	49.4		0.619	3.1	7.1

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	3ebr, 2oq1, 3bal, 3cjx	2.2	71.5	10021	512	86.17	0.17564	0.17342	0.17	0.21758	0.22	RANDOM	29.697

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]
-0.7	-0.35		-0.7		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.018
r_dihedral_angle_3_deg	19.201
r_dihedral_angle_4_deg	18.956
r_dihedral_angle_1_deg	7.77
r_angle_refined_deg	2.008
r_chiral_restr	0.132
r_bond_refined_d	0.019
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1234
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
BALBES	phasing
MOLREP	phasing
ARP	model building