8WEQ | pdb_00008weq

p-hydroxybenzoate 3-monooxygenase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.2M Magnesium chloride hexahydrate, 10% (v/v) Ethylene glycol, 0.1M HEPES pH 7.5, 15% (v/v) PEG Smear Medium, 5% (v/v) 2-Propanol

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.74	α = 90
b = 178.03	β = 116.167
c = 89.13	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	125	PIXEL	DECTRIS PILATUS3 6M		2022-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 11C	0.97942	PAL/PLS	11C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	3.29	29.901	96.94	0.997	14.19	6.8		33249

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.29	3.408			0.861

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.29	29.901	33249	1663	96.942	0.199	0.1955	0.1906	0.2558	0.2501	75.42

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]
5.163		0.685	-2.78		-2.061

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.03
r_dihedral_angle_4_deg	17.243
r_dihedral_angle_3_deg	16.65
r_lrange_other	8.212
r_lrange_it	8.211
r_scangle_it	7.615
r_scangle_other	7.615
r_dihedral_angle_1_deg	6.198
r_mcangle_other	5.893
r_mcangle_it	5.891
r_scbond_it	5.423
r_scbond_other	5.423
r_mcbond_it	3.936
r_mcbond_other	3.933
r_angle_other_deg	2.374
r_angle_refined_deg	1.908
r_nbd_other	0.375
r_symmetry_nbd_other	0.271
r_nbd_refined	0.243
r_xyhbond_nbd_refined	0.215
r_nbtor_refined	0.205
r_symmetry_nbd_refined	0.181
r_symmetry_xyhbond_nbd_other	0.125
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.083
r_bond_other_d	0.036
r_bond_refined_d	0.016
r_gen_planes_other	0.015
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12444
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	159

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing