2Q9T | pdb_00002q9t

High-resolution structure of the DING protein from Pseudomonas fluorescens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CAP	Human Phosphate-binding protein (HPBP) PDB code 2cap

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	24% PEG 8000, 100 mM acetate buffer pH 4.5, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.728	α = 90
b = 123.679	β = 116.71
c = 40.833	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 225 mm CCD		2006-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9535	ESRF	BM14

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	1.43	61.9	98.1	0.026	38.9	4	60045	59063			8.9

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	1.43	1.5	89.2		0.102	10.52	2.9	7166

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	Human Phosphate-binding protein (HPBP) PDB code 2cap	1.43	61.9	59063	2954	100	0.133	0.131	0.13	0.164	0.16	RANDOM	10.155

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]
-0.28		-0.19	-0.26		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.416
r_dihedral_angle_4_deg	12.15
r_dihedral_angle_3_deg	11.269
r_dihedral_angle_1_deg	5.714
r_sphericity_free	2.155
r_scangle_it	1.687
r_sphericity_bonded	1.51
r_scbond_it	1.206
r_angle_refined_deg	1.119
r_mcangle_it	0.869
r_rigid_bond_restr	0.617
r_mcbond_it	0.553
r_nbtor_refined	0.304
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.15
r_symmetry_hbond_refined	0.12
r_xyhbond_nbd_refined	0.095
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2698
Nucleic Acid Atoms
Solvent Atoms	766
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing