2V2L | pdb_00002v2l

Mutant (E53,56,57,60Q) recombinant horse spleen apoferritin cocrystallized with haemin in acidic conditions

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V2I	PDB ENTRY 2V2I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		RESERVOIR: CADMIUM SULFATE 0.13M, AMMONIUM SULFATE 0.8M, SODIUM ACETATE 0.1M PH 5.5, SODIUM AZIDE 0.003M. DROP: 2 UL PROTEIN AND 2 UL RESERVOIR

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.455	α = 90
b = 182.455	β = 90
c = 182.455	γ = 90

Symmetry
Space Group	F 4 3 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	MARRESEARCH	TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING.	2003-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	1.9	20	100	0.06	37.1	10.5		21041

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	1.9	1.94	99.9		0.49	5.3	7

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	PDB ENTRY 2V2I	1.9	105.41	19645	1064	98.2	0.19	0.188	0.2	0.216	0.22	RANDOM	19.95

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	37.377
r_dihedral_angle_4_deg	19.804
r_dihedral_angle_3_deg	13.44
r_dihedral_angle_1_deg	5.435
r_scangle_it	4.763
r_scbond_it	3.459
r_mcangle_it	1.758
r_mcbond_it	1.664
r_angle_refined_deg	1.556
r_angle_other_deg	0.991
r_symmetry_vdw_other	0.267
r_nbd_refined	0.239
r_symmetry_vdw_refined	0.233
r_nbd_other	0.193
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.168
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.102
r_nbtor_other	0.088
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	1372
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling