2JB3 | pdb_00002jb3

The structure of L-amino acid oxidase from Rhodococcus opacus in complex with o-aminobenzoate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.8		100MM HEPES PH 7.8 10% 2-PROPANOLE 10% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.4	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.649	α = 90
b = 109.676	β = 90
c = 134.368	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH		2004-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	1.85	30	99.2	0.15	9.5	4		83174

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	1.85	1.92	98.7		0.5	2	3.8

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 2JAE	1.85	19.77	78881	4145	99.2	0.154	0.151	0.16	0.214	0.22	RANDOM	15.16

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]
			-0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.674
r_dihedral_angle_4_deg	16.835
r_dihedral_angle_3_deg	12.529
r_dihedral_angle_1_deg	5.827
r_scangle_it	4.044
r_scbond_it	3.033
r_mcangle_it	1.837
r_mcbond_it	1.44
r_angle_other_deg	1.385
r_angle_refined_deg	1.341
r_gen_planes_other	0.219
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.196
r_nbd_other	0.184
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.184
r_symmetry_vdw_other	0.179
r_xyhbond_nbd_refined	0.175
r_nbtor_other	0.086
r_chiral_restr	0.084
r_gen_planes_refined	0.051
r_bond_refined_d	0.013
r_bond_other_d	0.002
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	7395
Nucleic Acid Atoms
Solvent Atoms	985
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing