2JB2 | pdb_00002jb2

The structure of L-amino acid oxidase from Rhodococcus opacus in complex with L-phenylalanine.

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 = 66.053	α = 90
b = 110.059	β = 90
c = 134.53	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	1.45	30	91.3	0.1	11.9	3.2		157853

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	1.45	1.5	86.1		0.48	2.1	2.9

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	1.45	14.99	149605	7886	91.2	0.173	0.172	0.18	0.199	0.21	RANDOM	14.12

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.946
r_dihedral_angle_4_deg	17.955
r_dihedral_angle_3_deg	11.122
r_dihedral_angle_1_deg	5.512
r_scangle_it	2.4
r_scbond_it	1.741
r_mcangle_it	1.175
r_angle_refined_deg	1.12
r_angle_other_deg	1.088
r_mcbond_it	0.981
r_gen_planes_other	0.228
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.206
r_nbtor_refined	0.18
r_nbd_other	0.167
r_symmetry_hbond_refined	0.162
r_symmetry_vdw_other	0.16
r_xyhbond_nbd_refined	0.124
r_nbtor_other	0.081
r_chiral_restr	0.066
r_gen_planes_refined	0.046
r_bond_refined_d	0.008
r_bond_other_d	0.001
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	7397
Nucleic Acid Atoms
Solvent Atoms	711
Heterogen Atoms	130

Software

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