3I09 | pdb_00003i09

CRYSTAL STRUCTURE OF A PERIPLASMIC BINDING PROTEIN (BMA2936) FROM BURKHOLDERIA MALLEI AT 1.80 A RESOLUTION

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	277	20.0000% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.255	α = 90
b = 81.151	β = 92.86
c = 73.996	γ = 90

Symmetry
Space Group	P 1 21 1

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 collimating mirror, toroid focusing mirror	2009-03-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97925,0.97903	SSRL	BL9-2

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	1.8	29.709	98.1	0.051	11.41	3.7		63635		-3	19.194

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	1.8	1.86	95.9		0.324	2.7

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	1.8	29.709	63613	3224	99.38	0.139	0.137	0.15	0.174	0.18	RANDOM	18.229

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]
-1.03		0.14	1.45		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.32
r_dihedral_angle_4_deg	22.65
r_dihedral_angle_3_deg	12.707
r_dihedral_angle_1_deg	5.85
r_scangle_it	4.287
r_scbond_it	2.617
r_angle_refined_deg	1.459
r_mcangle_it	1.414
r_angle_other_deg	0.906
r_mcbond_it	0.849

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.32
r_dihedral_angle_4_deg	22.65
r_dihedral_angle_3_deg	12.707
r_dihedral_angle_1_deg	5.85
r_scangle_it	4.287
r_scbond_it	2.617
r_angle_refined_deg	1.459
r_mcangle_it	1.414
r_angle_other_deg	0.906
r_mcbond_it	0.849
r_mcbond_other	0.384
r_chiral_restr	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5695
Nucleic Acid Atoms
Solvent Atoms	715
Heterogen Atoms	148

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.