6DLL | pdb_00006dll

2.2 Angstrom Resolution Crystal Structure of P-Hydroxybenzoate Hydroxylase from Pseudomonas putida in Complex with FAD.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	Protein: 13.8 mg/ml, 0.01M Tris HCl (pH 8.3), 1mM FAD; Screen: PACT (F4), 0.2M Potassium thiocyanate, 0.1M Bis-Tris propane (pH 6.5), 20% (w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.041	α = 90
b = 152.3	β = 102.43
c = 88.636	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD	C(111)	2016-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.2	30	100	0.059	0.059	0.067	0.031	23.8	4.5		86948		-3	44.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	100		0.805	0.805	0.915	0.431	0.779	1.94	4.5

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	1PBB	2.2	29.61	80878	4303	99.92	0.17013	0.1674	0.17	0.22167	0.22	RANDOM	43.517

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]
-1.14		-0.74	2.55		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.466
r_dihedral_angle_4_deg	12.301
r_dihedral_angle_3_deg	11.844
r_long_range_B_refined	5.598
r_long_range_B_other	5.571
r_dihedral_angle_1_deg	3.652
r_scangle_other	2.971
r_mcangle_it	2.12
r_mcangle_other	2.12
r_scbond_it	1.878
r_scbond_other	1.878
r_mcbond_it	1.384
r_mcbond_other	1.384
r_angle_refined_deg	1.284
r_angle_other_deg	0.444
r_chiral_restr	0.064
r_gen_planes_refined	0.04
r_gen_planes_other	0.037
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12554
Nucleic Acid Atoms
Solvent Atoms	895
Heterogen Atoms	226

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing