5IXR | pdb_00005ixr

Crystal Structure of C139A nostoc H-NOX domain with imidazole

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IAM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	1.9M sodium malonate, pH 7.0,

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.051	α = 90
b = 123.051	β = 90
c = 123.051	γ = 90

Symmetry
Space Group	P 21 3

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	MARMOSAIC 325 mm CCD	Mirrors	2012-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97945	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.5	43.51	99.45	0.049	24.2	6.2		20550			59.33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	100		2.3	6.3

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	4IAM	2.5	43.51	20550	1109	99.45	0.13282	0.13056	0.14	0.17353	0.18	RANDOM	59.313

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]
-17.46	8.93	-22.17	-19	-18.58	36.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.8
r_dihedral_angle_4_deg	18.839
r_dihedral_angle_3_deg	18.602
r_long_range_B_refined	10.029
r_long_range_B_other	10.028
r_scangle_other	7.422
r_mcangle_other	6.763
r_mcangle_it	6.756
r_dihedral_angle_1_deg	6.143
r_scbond_it	5.33
r_scbond_other	5.33
r_mcbond_it	4.68
r_mcbond_other	4.615
r_angle_refined_deg	1.718
r_angle_other_deg	0.897
r_chiral_restr	0.135
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2864
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	110

Software

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