1R7H | pdb_00001r7h

NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H75	PDB entry 1H75

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.86	293	Na-citrate, Tris, MPD, spermidine, pH 7.86, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.63	α = 90
b = 89.63	β = 90
c = 40.15	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2000-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.69	25	98.6			5187	5187

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.69	2.76	98.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1H75	2.69	23.7	5179	4942	237	98.31	0.24787	0.24513	0.24305	0.24	0.2876	0.29	RANDOM	30.383

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]
0.55	0.27		0.55		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.148
r_scangle_it	0.945
r_angle_refined_deg	0.894
r_angle_other_deg	0.694
r_mcangle_it	0.576
r_scbond_it	0.523
r_mcbond_it	0.311
r_symmetry_hbond_refined	0.307
r_symmetry_vdw_other	0.203
r_nbd_other	0.191
r_xyhbond_nbd_refined	0.183
r_nbd_refined	0.151
r_nbtor_other	0.083
r_symmetry_vdw_refined	0.08
r_chiral_restr	0.052
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1150
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing