5NC0

The 0.91 A resolution structure of the L16G mutant of cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitric oxide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YL7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	AMMONIUM SULPHATE, TRIS PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.43	α = 90
b = 52.43	β = 90
c = 183.25	γ = 120

Symmetry
Space Group	P 65 2 2

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	ADSC QUANTUM 315r		2010-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.78720	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	0.91	44.07	99.5	0.023	0.999	16.1	8		106845

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.91	0.93	93.9		0.564	0.547	1.3	4.4

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	2YL7	0.91	44.07	101466	5378	99.29	0.1249	0.12453	0.13	0.13177	0.14	RANDOM	8.977

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]
-0.15	-0.07		-0.15		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.774
r_sphericity_free	19.653
r_dihedral_angle_4_deg	11.307
r_dihedral_angle_3_deg	11.017
r_sphericity_bonded	6.354
r_rigid_bond_restr	5.075
r_dihedral_angle_1_deg	4.75
r_long_range_B_refined	2.578
r_long_range_B_other	2.577
r_angle_refined_deg	2.471
r_scangle_other	1.816
r_scbond_it	1.53
r_scbond_other	1.53
r_angle_other_deg	1.075
r_mcangle_other	0.984
r_mcangle_it	0.976
r_mcbond_it	0.716
r_mcbond_other	0.623
r_chiral_restr	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	936
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing