2RI6 | pdb_00002ri6

Crystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	1.9 M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.293	α = 90
b = 117.293	β = 90
c = 87.306	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		2005-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	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	1.68	50	99.8	12.6	18.6	12.3		34855	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	1.68	1.74	99.3		27.1	8.1	11.8	3424

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		THROUGHOUT	1.68	44.95	34845	1752	99.75	0.176	0.175	0.1778	0.201	0.204	RANDOM	18.094

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]
0.22			0.22		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.767
r_dihedral_angle_4_deg	17.194
r_dihedral_angle_3_deg	13.847
r_scangle_it	11.428
r_scbond_it	9.153
r_mcangle_it	5.715
r_dihedral_angle_1_deg	5.484
r_mcbond_it	3.919
r_angle_refined_deg	1.218
r_nbtor_refined	0.307
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.188
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2239
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	15

Software

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