4YEH | pdb_00004yeh

Crystal structure of Mg2+ ion containing hemopexin fold from Kabuli chana (chickpea white) at 2.45A resolution reveals a structural basis of metal ion transport

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HSD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.2M Magnesium acetate tetra hydrate, 0.1M sodiun cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.481	α = 90
b = 80.481	β = 90
c = 69.177	γ = 120

Symmetry
Space Group	P 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MARRESEARCH		2012-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	2.45	69.7	100	0.14	5.3	4.1	17005	17005

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	2.45	2.54	97		0.487	2.4

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 (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	4HSD	2.45	69.7	17005	890	96.96	0.15284	0.15066	0.16	0.19388	0.19	RANDOM	21.079

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]
3.36			3.36		-6.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.2
r_dihedral_angle_3_deg	19.981
r_dihedral_angle_4_deg	17.532
r_dihedral_angle_1_deg	8.132
r_long_range_B_refined	4.831
r_mcangle_it	2.58
r_angle_refined_deg	1.992
r_scbond_it	1.829
r_mcbond_it	1.692
r_chiral_restr	0.134
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3592
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALEPACK	data scaling
Coot	model building