2JE2 | pdb_00002je2

Cytochrome P460 from Nitrosomonas europaea - probable nonphysiological oxidized form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		INITIAL MODEL FROM SULPHUR SAD STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.2		pH 5.20

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.256	α = 90
b = 53.256	β = 90
c = 127.033	γ = 120

Symmetry
Space Group	P 31 2 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	IMAGE PLATE	RIGAKU IMAGE PLATE	VARIMAX CONFOCAL MAXFLUX	2005-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	1.69	43	80.9	0.04	17.7	2.9		17631		2	25.3

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	1.69	1.75	13.5		0.1	2.8	1.1

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-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	INITIAL MODEL FROM SULPHUR SAD STRUCTURE	1.8	43.36	17631	952	92.5	0.199	0.197	0.19	0.237	0.23	RANDOM	26.3

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.586
r_dihedral_angle_4_deg	21.394
r_dihedral_angle_3_deg	14.826
r_dihedral_angle_1_deg	8.107
r_scangle_it	3.398
r_scbond_it	2.283
r_mcangle_it	1.756
r_angle_refined_deg	1.641
r_mcbond_it	1.023
r_nbtor_refined	0.304
r_nbd_refined	0.27
r_symmetry_vdw_refined	0.176
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.142
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1223
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling