2OC5 | pdb_00002oc5

Crystal structure of a ferritin-like protein (pmt1231) from prochlorococcus marinus str. mit 9313 at 1.68 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	7.8	277	0.2M KAcetate, 20.0% PEG-3350, No Buffer pH 7.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.35	α = 90
b = 77.35	β = 90
c = 116.89	γ = 90

Symmetry
Space Group	P 43 21 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 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2006-12-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162, 0.97929, 0.97915	SSRL	BL9-2

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	1.68	29.235	99.6	0.069	10.19			41123			30.354

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	1.68	1.74	97.2		0.545	2.08		7028

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.68	29.235	40994	2060	99.48	0.166	0.164	0.17	0.2	0.21	RANDOM	21.126

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]
0.07			0.07		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.751
r_dihedral_angle_4_deg	18.408
r_dihedral_angle_3_deg	12.293
r_scangle_it	6.366
r_scbond_it	4.79
r_dihedral_angle_1_deg	4.584
r_mcangle_it	2.734
r_mcbond_it	2.03
r_angle_refined_deg	1.472
r_angle_other_deg	0.893
r_mcbond_other	0.561
r_symmetry_vdw_other	0.363
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.201
r_symmetry_vdw_refined	0.2
r_symmetry_hbond_refined	0.199
r_nbtor_refined	0.182
r_nbd_other	0.175
r_chiral_restr	0.091
r_nbtor_other	0.083
r_metal_ion_refined	0.02
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1736
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	26

Software

Software
Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction