1YVI

X-RAY STRUCTURE OF PUTATIVE HISTIDINE-CONTAINING PHOSPHOTRANSFER PROTEIN FROM RICE, AK104879

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WN0	PDB ENTRY 1WN0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	293	10 MG/ML PROTEIN, 1.0 M SODIUM CITRATE, 0.10 M PIPES, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.558	α = 90
b = 100.558	β = 90
c = 69.568	γ = 90

Symmetry
Space Group	P 43 21 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	APS-1	SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR	2004-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	37.77	98.9	0.105	16.747	8.4		24495

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)
	2	2.05	99.5		0.596	3.521	7.2

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1WN0	2	37.77	23200	1249	98.95	0.175	0.17525	0.17246	0.2272	RANDOM	23.782

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]
0.11			0.11		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.971
r_dihedral_angle_4_deg	21.838
r_dihedral_angle_3_deg	14.908
r_scangle_it	8.329
r_scbond_it	5.61
r_dihedral_angle_1_deg	5.033
r_mcangle_it	3.53
r_mcbond_it	2.939
r_angle_refined_deg	1.609
r_nbtor_refined	0.308
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.118
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2183
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
ARP/wARP	model building