4G78 | pdb_00004g78

Subatomic Resolution Crystal Structure of Histidine-containing Phosphotransfer Protein MtHPt2 from Medicago truncatula

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3US6	PDB ENTRY 3US6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	292	0.09M Halogens, 0.1M buffer system 1, 30% PEG 550MME + PEG 20K (Molecular Dimensions Morpheus Screen B1), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
1.81	32.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.24	α = 90
b = 50.15	β = 97.44
c = 50.38	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	FOCUSING MIRRORS	2012-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	0.92	50	97.8	0.036	21.78	6.3		84634		-3	13.232

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	0.92	0.94	75.1		0.738	1.89

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	R-FREE	PDB ENTRY 3US6	0.92	50	84634	79313	1008	97.8	0.121	0.121	0.13	0.155	0.16	RAMDOM	19.627

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
s_from_restr_planes	0.3
s_non_zero_chiral_vol	0.157
s_angle_d	0.04
s_bond_d	0.023
s_similar_dist
s_zero_chiral_vol
s_anti_bump_dis_restr
s_rigid_bond_adp_cmpnt
s_similar_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1182
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
SHELX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXL-97	refinement

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.