2C12 | pdb_00002c12

Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C0U	PDB ENTRY 2C0U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		25%(W/V) PEG 4000, 35% (V/V) GLYCEROL, 200 MM SODIUM CACODYLATE TRIHYDRATE PH 7.5, 1 MM SPERMINE TETRAHYDROCHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.393	α = 90
b = 103.393	β = 90
c = 485.134	γ = 120

Symmetry
Space Group	P 32 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	CCD	ADSC CCD		2003-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C

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	2.07	50	97.8	0.14	12.6	1.64		180533		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	2.07	2.15	81.9		0.269	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-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 2C0U	2.07	50	171484	9048	97.8	0.19	0.188	0.2	0.225	0.24	RANDOM	24.66

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]
0.68	0.34		0.68		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.422
r_scangle_it	3.13
r_scbond_it	1.874
r_angle_refined_deg	1.394
r_mcangle_it	1.11
r_angle_other_deg	0.992
r_mcbond_it	0.575
r_symmetry_vdw_other	0.254
r_nbd_other	0.244
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.201
r_symmetry_hbond_refined	0.18
r_symmetry_vdw_refined	0.156
r_nbtor_other	0.086
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
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	19842
Nucleic Acid Atoms
Solvent Atoms	1117
Heterogen Atoms	512

Software

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