2G2P | pdb_00002g2p

Crystal Structure of E.coli transthyretin-related protein with bound Zn and Br

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F41

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	25% PEG 550 MME, 100mM MES, 10mM ZnSO4 (Crystal soaked in crystallization buffer enriched with 100mM NaBr for 12h prior to data collection), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.72	α = 90
b = 92.03	β = 103.5
c = 57.49	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	MARRESEARCH		2001-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8033	EMBL/DESY, HAMBURG	X13

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	2.1	20	96.3	0.047	27.1		25512	25512

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	2.1	2.3	93.6		0.2	10

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	1F41	2.1	17.38	24310	24310	1300	97.51	0.17752	0.17752	0.17482	0.18	0.22903	0.23	RANDOM	19.438

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]
		0.04	0.03		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.731
r_scangle_it	2.583
r_scbond_it	1.759
r_angle_refined_deg	1.334
r_mcangle_it	0.941
r_angle_other_deg	0.768
r_mcbond_it	0.516
r_symmetry_vdw_refined	0.283
r_symmetry_vdw_other	0.272
r_nbd_other	0.244
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.187
r_metal_ion_refined	0.178
r_xyhbond_nbd_refined	0.155
r_nbtor_other	0.086
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3618
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling