4ISM | pdb_00004ism

Crystal structure of ferritin from Pseudo-nitzschia multiseries soaked with zinc

X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.112	α = 90
b = 175.112	β = 90
c = 175.112	γ = 90

Symmetry
Space Group	P 2 3

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

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	2	50	99.9	0.086	14.2	14.7		120229

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	2.07	100		0.452		14.6	11937

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	2	42.51	117223	5893	97.52	0.1861	0.1837	0.1791	0.2315	0.2254	RANDOM	30.0452

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	41.068
r_dihedral_angle_4_deg	19.146
r_dihedral_angle_3_deg	15.176
r_dihedral_angle_1_deg	5.297
r_scbond_it	4.421
r_mcangle_it	3.612
r_mcbond_it	2.829
r_angle_refined_deg	1.94
r_chiral_restr	0.148
r_bond_refined_d	0.021

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.068
r_dihedral_angle_4_deg	19.146
r_dihedral_angle_3_deg	15.176
r_dihedral_angle_1_deg	5.297
r_scbond_it	4.421
r_mcangle_it	3.612
r_mcbond_it	2.829
r_angle_refined_deg	1.94
r_chiral_restr	0.148
r_bond_refined_d	0.021
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10016
Nucleic Acid Atoms
Solvent Atoms	912
Heterogen Atoms	32

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.