1E85 | pdb_00001e85

Cytochrome c' from Alcaligenes xylosoxidans - reduced structure with NO bound to proximal side of heme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CGO	PDB ENTRY 1CGO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5. REDUCED USING MOTHER LIQUOR CONTAINING 20 MM SODIUM DITHIONITE, THEN INCUBATED FOR 6 DAYS IN MOTHER LIQUOR SATURATED WITH NO.

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.035	α = 90
b = 53.035	β = 90
c = 180.993	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 CCD	MIRRORS	2000-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.35	40	98.8	0.039	39.8	6.8		33925		-3	16

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	1.35	1.37	93.1		0.227	3.9

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1CGO	1.35	40	33925	1732	98.8	0.194	0.19	0.22	RANDOM	18

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	27.4
p_staggered_tor	12.8
p_planar_tor	4.3
p_scangle_it	3.959
p_scbond_it	2.867
p_mcangle_it	1.623
p_mcbond_it	1.238
p_multtor_nbd	0.267
p_singtor_nbd	0.17
p_xyhbond_nbd	0.14
p_chiral_restr	0.092
p_planar_d	0.03
p_angle_d	0.024
p_plane_restr	0.0239
p_bond_d	0.011
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	927
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	45

Software

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