2V2P | pdb_00002v2p

Mutant (E53,56,57,60Q and R59M) 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	2V2L	PDB ENTRY 2V2L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		RESERVOIR: CADMIUM SULFATE 0.08M, AMMONIUM SULFATE 0.5M, SODIUM ACETATE 0.1M PH 5.6, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.255	α = 90
b = 181.255	β = 90
c = 181.255	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	MIRROR 2 BENT, VERTICALLY FOCUSSING	2007-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		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	1.15	23	98.4	0.06	14	6.8		88729

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	1.15	1.2	87.8		0.46	3	3.8

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2V2L	1.15	104.83	84284	4440	98.7	0.201	0.199	0.21	0.224	RANDOM	11.58

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	37.935
r_dihedral_angle_4_deg	17.96
r_dihedral_angle_3_deg	11.437
r_scangle_it	5.836
r_dihedral_angle_1_deg	4.695
r_scbond_it	4.421
r_mcangle_it	2.593
r_mcbond_it	2.366
r_angle_refined_deg	1.666
r_angle_other_deg	0.981
r_nbd_refined	0.266
r_symmetry_vdw_refined	0.262
r_symmetry_vdw_other	0.241
r_xyhbond_nbd_refined	0.22
r_nbd_other	0.204
r_nbtor_refined	0.19
r_symmetry_hbond_refined	0.18
r_chiral_restr	0.105
r_nbtor_other	0.093
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.002
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	1360
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	22

Software

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