2HPG | pdb_00002hpg

The crystal structure of a thermophilic TRAP periplasmic binding protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	290	0.1M Phosphate/Citrate pH4.2, 2.5M Ammonium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.26	α = 90
b = 119.26	β = 90
c = 429.1	γ = 120

Symmetry
Space Group	P 65 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 300 mm CCD		2005-03-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97167, 0.97934, 0.97920	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	103.282	100	0.094	0.094	6.2	9.6	142555	142555

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)
	1.9	2	100		0.405	0.405	1.9	8.4	20471

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD	THROUGHOUT	1.9	30	142411	142411	7152	100	0.215	0.215	0.213	0.2183	0.239	0.243	RANDOM	23.493

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]
1.1	0.55		1.1		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.398
r_dihedral_angle_4_deg	17.595
r_dihedral_angle_3_deg	14.701
r_dihedral_angle_1_deg	5.844
r_scangle_it	2.561
r_scbond_it	1.751
r_angle_refined_deg	1.249
r_mcangle_it	1.017
r_mcbond_it	0.875
r_angle_other_deg	0.872
r_symmetry_vdw_refined	0.263
r_symmetry_vdw_other	0.241
r_nbd_refined	0.21
r_nbd_other	0.183
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.162
r_symmetry_hbond_refined	0.154
r_mcbond_other	0.13
r_nbtor_other	0.085
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10353
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
CCP4	data scaling
SHELXS	phasing