4IWK | pdb_00004iwk

Crystal structure of iron soaked (overnight) ferritin from Pseudo-nitzschia multiseries

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5		pH 5.5, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
3	58.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.251	α = 90
b = 126.251	β = 90
c = 170.299	γ = 90

Symmetry
Space Group	P 4 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		CCD	ADSC QUANTUM 315r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1	SSRL	BL7-1

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	1.65	50	99.6	0.065	16.8	10.7		164004

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	1.65	1.71	100		0.507		6.4	16255

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.65	47.95	163306	8206	99.17	0.1772	0.1757	0.174	0.2046	0.2029	RANDOM	25.5402

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]
0.11			0.11		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.15
r_dihedral_angle_4_deg	17.518
r_dihedral_angle_3_deg	14.213
r_dihedral_angle_1_deg	5.121
r_scbond_it	4.529
r_mcangle_it	3.368
r_mcbond_it	2.522
r_angle_refined_deg	2.493
r_chiral_restr	0.189
r_bond_refined_d	0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.15
r_dihedral_angle_4_deg	17.518
r_dihedral_angle_3_deg	14.213
r_dihedral_angle_1_deg	5.121
r_scbond_it	4.529
r_mcangle_it	3.368
r_mcbond_it	2.522
r_angle_refined_deg	2.493
r_chiral_restr	0.189
r_bond_refined_d	0.028
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7533
Nucleic Acid Atoms
Solvent Atoms	872
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.