2CHP | pdb_00002chp

Crystal structure of the dodecameric ferritin MrgA from B. subtilis 168

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		MRGA MUTANT

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.37	α = 90
b = 125.37	β = 90
c = 125.37	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591

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	87.71	95.4	0.08	8.6	4.4		44572		-3

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	2.1	88		0.32	2.2	4.2

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	MRGA MUTANT	2	87.71	41011	1262	95	0.157	0.155	0.17	0.208	0.22	RANDOM	16.97

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.704
r_dihedral_angle_4_deg	18.733
r_dihedral_angle_3_deg	12.81
r_dihedral_angle_1_deg	5.2
r_scangle_it	4.199
r_scbond_it	3.129
r_angle_refined_deg	1.772
r_mcangle_it	1.658
r_mcbond_it	1.477
r_angle_other_deg	1.314
r_symmetry_vdw_refined	0.61
r_symmetry_hbond_refined	0.307
r_symmetry_vdw_other	0.302
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.185
r_nbd_other	0.174
r_chiral_restr	0.161
r_nbtor_other	0.086
r_bond_refined_d	0.026
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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_other
r_long_range_B_refined
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	4685
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing