2PU5 | pdb_00002pu5

Crystal Structure of a C-C bond hydrolase, BphD, from Burkholderia xenovorans LB400

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.0 M sodium, malonate, pH 6.0 or 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.183	α = 90
b = 135.183	β = 90
c = 66.268	γ = 120

Symmetry
Space Group	P 64

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 300 mm CCD		2005-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	50	99.8	12.4	12.2	6.3		30870		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3		98.6		33.2	3.4	3.5	3046

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.3		29262	30815	1553	99.58	0.18	0.176	0.1851	0.27	0.2685	RANDOM	48.757

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]
0.41	0.21		0.41		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.589
r_scbond_it	24.35
r_scangle_it	22.857
r_mcangle_it	19.867
r_mcbond_it	19.58
r_dihedral_angle_3_deg	18.825
r_dihedral_angle_4_deg	18.6
r_dihedral_angle_1_deg	7.66
r_angle_refined_deg	2.022
r_symmetry_hbond_refined	0.422
r_nbtor_refined	0.331
r_nbd_refined	0.261
r_xyhbond_nbd_refined	0.255
r_symmetry_vdw_refined	0.213
r_chiral_restr	0.132
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4492
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	14

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing