2NUK | pdb_00002nuk

Soluble Domain of the Rieske Iron-Sulfur Protein from Rhodobacter sphaeroides

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NWF	pdb entry 2NWF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	278	1.5 M Ammonium sulfate, 20% anhydrous glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.568	α = 90
b = 70.568	β = 90
c = 54.769	γ = 90

Symmetry
Space Group	I 4

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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	1.2	12	98	0.02	24.7	4.2	41254	41254	2	2

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	1.24	99.7		0.065	19.6	4.2	4192

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 2NWF	1.2	11.67	38022	3177	98.16	0.11969	0.11828	0.13	0.13639	0.15	RANDOM	9.781

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]
-0.02			-0.02		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.503
r_sphericity_free	21.201
r_dihedral_angle_4_deg	11.87
r_dihedral_angle_3_deg	8.532
r_dihedral_angle_1_deg	5.089
r_sphericity_bonded	2.547
r_scangle_it	1.869
r_angle_refined_deg	1.738
r_mcangle_it	1.513
r_scbond_it	1.363
r_mcbond_it	1.145
r_angle_other_deg	0.953
r_rigid_bond_restr	0.747
r_mcbond_other	0.533
r_symmetry_vdw_refined	0.302
r_nbd_refined	0.231
r_nbd_other	0.192
r_nbtor_refined	0.17
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.126
r_symmetry_vdw_other	0.122
r_chiral_restr	0.09
r_nbtor_other	0.083
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2153
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing