2DU2 | pdb_00002du2

Crystal Structure Analysis of the L-Lactate Oxidase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	18-20%(w/v) PEG 8000, 50mM Tris buffer pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 191.096	α = 90
b = 191.096	β = 90
c = 194.497	γ = 90

Symmetry
Space Group	I 4 2 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	CCD	ADSC QUANTUM 4		2004-12-10	M	SINGLE WAVELENGTH
2	1	100	IMAGE PLATE	MAC Science, DIP6040
3	1	100	CCD	MARRESEARCH
4	1	100	CCD	ADSC QUANTUM 4

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1
2	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	1.0	SPring-8	BL44XU
3	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU
4	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	46	100	0.142	22.72	12.8	108566	108566	1	1	19.47

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)
	2.07	2.14	100		0.436

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1GOX	2.1	20	1	1	103006	103006	5418	100	0.16168	0.16168	0.1597	0.16	0.19904	0.16	RANDOM	19.443

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]
0.32			0.32		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.092
r_dihedral_angle_4_deg	17.615
r_dihedral_angle_3_deg	16.219
r_dihedral_angle_1_deg	6.865
r_scangle_it	4.002
r_scbond_it	2.639
r_angle_refined_deg	1.781
r_mcangle_it	1.587
r_mcbond_it	1.007
r_nbtor_refined	0.312
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.188
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.141
r_chiral_restr	0.132
r_bond_refined_d	0.018
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11552
Nucleic Acid Atoms
Solvent Atoms	1109
Heterogen Atoms	124

Software

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