2BP0 | pdb_00002bp0

M144L mutant of nitrite reductase from Alcaligenes xylosoxidans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OE1	PDB ENTRY 1OE1

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.605	α = 90
b = 90.605	β = 90
c = 291.439	γ = 120

Symmetry
Space Group	H 3

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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6		SRS	PX9.6

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	1.9	70	97.4	0.08	18	3.2		69754

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	91.4		3.2

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	PDB ENTRY 1OE1	1.9	70	65115	3451	97.5	0.161	0.159	0.17	0.196	0.21	RANDOM	22.32

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.17
r_scangle_it	3.608
r_scbond_it	2.312
r_angle_refined_deg	1.537
r_mcangle_it	1.482
r_angle_other_deg	0.897
r_mcbond_it	0.854
r_symmetry_hbond_refined	0.395
r_symmetry_vdw_other	0.306
r_nbd_other	0.238
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.207
r_symmetry_vdw_refined	0.183
r_chiral_restr	0.104
r_nbtor_other	0.079
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	5086
Nucleic Acid Atoms
Solvent Atoms	791
Heterogen Atoms	40

Software

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