3D9D | pdb_00003d9d

Nitroalkane oxidase: mutant D402N crystallized with 1-nitrohexane

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C12

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	20-30mM PEG 3350, 20-35% glycerol, 0.1M NaCacodylate, pH 7.50, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.875	α = 90
b = 107.875	β = 90
c = 338.442	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 QUANTUM 270	mirrors	2007-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B	1.1	NSLS	X12B

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	2.1	50	91.9	0.089	0.089	13.72	3.2	391270	391270	-3

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	2.1	2.18	62.1		0.447	0.447	1.2	1.6	8209

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLREP	THROUGHOUT	2c12	2.1	50	133933	123030	6169	91.86	0.182	0.182	0.18	0.219	0.2101	RANDOM	36.174

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]
0.31	0.15		0.31		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.101
r_dihedral_angle_4_deg	18.29
r_dihedral_angle_3_deg	16.079
r_dihedral_angle_1_deg	5.454
r_scangle_it	3.635
r_scbond_it	2.362
r_angle_refined_deg	1.525
r_mcangle_it	1.292
r_mcbond_it	1.158
r_symmetry_hbond_refined	0.428
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.282
r_nbd_refined	0.209
r_chiral_restr	0.138
r_xyhbond_nbd_refined	0.128
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13219
Nucleic Acid Atoms
Solvent Atoms	650
Heterogen Atoms	296

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing