2HZK | pdb_00002hzk

Crystal structures of a sodium-alpha-keto acid binding subunit from a TRAP transporter in its open form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	293	100 mM sodium citrate 1.5M ammonium sulfate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.505	α = 90
b = 63.826	β = 106.58
c = 127.897	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		2006-02-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97940,0.97960,0.97565	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	60	99			177747	175128	1	1

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	1.7	1.71	95.5

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	1.7	60	177747	175128	8721	98.53	0.18	0.18	0.179	0.1782	0.206	0.2047	RANDOM	17.167

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]
0.24		0.3	0.33		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.013
r_dihedral_angle_4_deg	15.53
r_dihedral_angle_3_deg	14.182
r_dihedral_angle_1_deg	5.575
r_scangle_it	3.296
r_scbond_it	2.393
r_angle_refined_deg	1.309
r_mcangle_it	1.261
r_mcbond_it	1.058
r_nbtor_refined	0.309
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.16
r_symmetry_hbond_refined	0.112
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.108
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10511
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms	24

Software

Software
Software Name	Purpose
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling