8GDW | pdb_00008gdw

Crystal structure of Domain Related to Iron (DRI) from cyanobacteria

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5BNC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	25% PEG3350, 100 mM Bis-Tris, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.716	α = 90
b = 87.23	β = 94.981
c = 57.241	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2019-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.9793	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.35	29.5	99	0.055	0.99	15	5.3		20972			56.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.41	87.8		0.736	0.76	1.9	5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 5BNC	2.35	29.5	20954	1027	98.989	0.199	0.197	0.2	0.2474	0.25	61.989

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]
-0.376		2.54	-3.183		3.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.667
r_dihedral_angle_3_deg	21.944
r_dihedral_angle_4_deg	21.056
r_lrange_it	12.529
r_lrange_other	12.529
r_scangle_it	8.698
r_scangle_other	8.696
r_mcangle_it	8.181
r_mcangle_other	8.178
r_dihedral_angle_1_deg	6.696
r_scbond_it	5.644
r_scbond_other	5.642
r_mcbond_other	5.427
r_mcbond_it	5.425
r_angle_refined_deg	1.545
r_angle_other_deg	1.341
r_nbd_other	0.24
r_symmetry_nbd_refined	0.224
r_nbd_refined	0.21
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_refined	0.138
r_symmetry_xyhbond_nbd_other	0.113
r_symmetry_nbtor_other	0.089
r_metal_ion_refined	0.085
r_chiral_restr	0.059
r_symmetry_metal_ion_refined	0.011
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3096
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing