3E99 | pdb_00003e99

Crystal structure of the beta subunit of the benzoate 1,2-dioxygenase (benb, bmaa0186) from burkholderia mallei atcc 23344 at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	15.0000% Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000, 0.1M TRIS pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.953	α = 90
b = 58.953	β = 90
c = 167.073	γ = 120

Symmetry
Space Group	P 63 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-07-31	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97822,0.97901	SSRL	BL11-1

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	1.9	29.476	99.6	0.073	7.03	5.2		14285			26.262

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	100		0.509	0.509	0.568	1.4	5.3	1022

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.9	29.476	14242	717	99.17	0.188	0.186	0.19	0.223	0.23	RANDOM	30.839

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.707
r_dihedral_angle_4_deg	15.907
r_dihedral_angle_3_deg	12.99
r_dihedral_angle_1_deg	6.342
r_scangle_it	5.892
r_scbond_it	4.966
r_mcangle_it	3.099
r_mcbond_it	2.095
r_angle_refined_deg	1.46
r_angle_other_deg	0.911
r_mcbond_other	0.566
r_symmetry_vdw_other	0.281
r_symmetry_hbond_refined	0.222
r_nbd_other	0.219
r_nbd_refined	0.199
r_nbtor_refined	0.192
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.093
r_nbtor_other	0.084
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1225
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	4

Software

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