3U1W

Crystal structure of a Calcium binding protein (BDI_1975) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	20.0% 2-propanol, 0.2M calcium chloride, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.33	71.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.258	α = 90
b = 152.84	β = 90
c = 165.691	γ = 90

Symmetry
Space Group	I 2 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	Vertical focusing mirror; double crystal Si(111) monochromator	2011-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1		SSRL	BL14-1

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	29.99	100	0.141	8.4	6.3	101909	101909

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	100		0.995	0.995	0.7	6.3	7476

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	29.99	101900	5088	99.93	0.1906	0.1893	0.2147	RANDOM	34.4015

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]
2.49			-0.65		-1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.499
r_dihedral_angle_3_deg	9.13
r_dihedral_angle_4_deg	5.902
r_torsion_it	4.319
r_dihedral_angle_1_deg	3.405
r_angle_it	2.375
r_bond_it	1.459
r_angle_refined_deg	1.401
r_angle_others	1.345
r_angle_other_deg	0.795

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.499
r_dihedral_angle_3_deg	9.13
r_dihedral_angle_4_deg	5.902
r_torsion_it	4.319
r_dihedral_angle_1_deg	3.405
r_angle_it	2.375
r_bond_it	1.459
r_angle_refined_deg	1.401
r_angle_others	1.345
r_angle_other_deg	0.795
r_bond_other	0.272
r_chiral_restr	0.055
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5983
Nucleic Acid Atoms
Solvent Atoms	826
Heterogen Atoms	59

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	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 R01GM133198.