2PU7

Crystal Structure of S112A/H265A double mutant of a C-C 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	6.5	293	1.9 M sodium malonate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.361	α = 90
b = 116.361	β = 90
c = 87.942	γ = 90

Symmetry
Space Group	I 41 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 300 mm CCD		2006-07-05	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	2.07	82.2	98.8	8.4	23.9	9.3		18453	2	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	2.07	2.125	92.4		8.4	3	6.7	1697

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2OG1	2.07	82.2	17503	18447	944	98.82	0.182	0.178	0.258	RANDOM	28.257

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]
1.21			1.21		-2.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.761
r_scangle_it	17.546
r_scbond_it	16.841
r_dihedral_angle_4_deg	16.242
r_dihedral_angle_3_deg	15.993
r_mcangle_it	11.194
r_mcbond_it	10.29
r_dihedral_angle_1_deg	5.994
r_angle_refined_deg	1.592
r_symmetry_metal_ion_refined	0.315
r_nbtor_refined	0.31
r_metal_ion_refined	0.266
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.209
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.102
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2234
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	15

Software

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