2V15 | pdb_00002v15

Terbium binding in Streptococcus suis Dpr protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UMN	PDB ENTRY 1UMN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	289	2UL AND 2UL VOLUME DROP, 30 % PEG 400, 0.2 M CACL2, 0.1 M HEPES-NAOH, PH 7.4, HANGING DROP,16C

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.485	α = 90
b = 137.715	β = 90
c = 142.438	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH	MIRRORS	2004-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711		MAX II	I711

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	2	28	95.6	0.08	13.9	5.4		115331		4.57

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UMN	2.1	19.98	109570	5761	100	0.19	0.188	0.19	0.244	0.25	RANDOM	33.76

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.158
r_dihedral_angle_3_deg	15.754
r_dihedral_angle_4_deg	14.232
r_dihedral_angle_1_deg	4.91
r_scangle_it	3.87
r_scbond_it	2.513
r_mcangle_it	1.468
r_angle_refined_deg	1.412
r_mcbond_it	0.93
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.174
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14509
Nucleic Acid Atoms
Solvent Atoms	619
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL	data reduction
SCALEPACK	data scaling