1H9Y | pdb_00001h9y

Cytochrome cd1 Nitrite Reductase, reduced form complexed to CN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H9X	PDB ENTRY 1H9X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9		HANGING DROP USING 2.1 M AMMONIUM SULPHATE AND 100 MM CHES PH 7.0 1 MM ASCORMBATE AND 2.5 UM PMS FROM REDUCTION OF PROTEIN WAS ALSO PRESENT IN CRYSTALLISATION.

Crystal Properties
Matthews coefficient	Solvent content
4.3	71.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.573	α = 90
b = 127.573	β = 90
c = 263.201	γ = 90

Symmetry
Space Group	P 43 21 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	IMAGE PLATE	MARRESEARCH		2000-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711		MAX II	I711

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	2.4	20	97.9	0.086	0.086	16.4	3.2		83427			43.6

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	2.4	2.49	93		0.287	0.287	3.1

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 1H9X	2.4	20	83427		99.7	0.238	0.21	0.269	RANDOM	40.2

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	31.6
p_special_tor	15
p_staggered_tor	14.9
p_planar_tor	3
p_chiral_restr	0.98
p_multtor_nbd	0.243
p_singtor_nbd	0.184
p_xyhbond_nbd	0.16
p_bond_d	0.08
p_angle_d	0.026
p_planar_d	0.024
p_plane_restr	0.0047
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	8107
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	202

Software

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