1HJ4 | pdb_00001hj4

Cytochrome cd1 Nitrite Reductase, x-ray reduced dioxygen complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	293	2.3 M AMMONIUM SULFATE 50MM POTASSIUM PHOSPHATE PH 7.0 CRYSTALS WERE REDUCED USING 20MM SODIUM DITHIONITE. THE CRYSTAL WAS TRANSFERRED TO A SOLUTION CONTAINING 2.3 M AMMONIUM SULFATE, 50 MM PHOSPAHTE BUFFER PH 7 AND 15 % GLYCEROL. O2 WAS INTRODUCED UNDER 15 ATM PRESSURE FOR 2 MINUTES AT -20 DEGREES. THE DIOXYGEN SPECIES FORMED UNDER THESE CONDITIONS WAS REDUCED UPON X-RAY EXPOSURE AND THE RESULTING STRUCTURE REPRESENTS A MIXTURE OF STATES.

Crystal Properties
Matthews coefficient	Solvent content
2.52	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.69	α = 90
b = 60.9	β = 112.08
c = 100.59	γ = 90

Symmetry
Space Group	P 1 21 1

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		1998-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.6	30	93.9	0.041	0.041	14.2	2.2		149315			18.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	95.3		0.202	0.202	2.8

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1AOF	1.6	30	149315		93.9	0.202	0.226	RANDOM

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	29.3
p_special_tor	15
p_staggered_tor	10.9
p_planar_tor	4.2
p_multtor_nbd	0.24
p_singtor_nbd	0.18
p_xyhbond_nbd	0.152
p_chiral_restr	0.117
p_plane_restr	0.026
p_planar_d	0.024
p_angle_d	0.015
p_bond_d	0.013
p_angle_deg
p_hb_or_metal_coord
p_mcbond_it
p_mcangle_it
p_scbond_it
p_scangle_it
p_xhyhbond_nbd
p_orthonormal_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8497
Nucleic Acid Atoms
Solvent Atoms	889
Heterogen Atoms	211

Software

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