3MIG | pdb_00003mig

Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound nitrite, obtained in the presence of substrate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	Crystallization: 0.1-0.5mM CuSO4, 1.25mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. The crystal was first soaked in 1mM substrate (Ac-3,5-diI-YG) for 1 hour and then soaked in 300mM NaNO2/1mM substrate for 14 hours at 293K., VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.356	α = 90
b = 68.783	β = 90
c = 79.979	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	MAR scanner 345 mm plate		2007-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.98	NSLS	X4C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.7	52	99	0.085	35.7	7		10776		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.8	91.4		0.53	2.1	5.6	970

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 1PHM	2.7	52	10216	518	98.86	0.22387	0.22146	0.21	0.27236	0.26	RANDOM	60.565

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]
0.56			-3.61		3.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.537
r_dihedral_angle_3_deg	15.739
r_dihedral_angle_4_deg	15.181
r_dihedral_angle_1_deg	6.474
r_scangle_it	1.496
r_angle_refined_deg	1.221
r_scbond_it	0.957
r_mcangle_it	0.674
r_mcbond_it	0.416
r_nbtor_refined	0.311
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.181
r_symmetry_hbond_refined	0.148
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_metal_ion_refined	0.007
r_gen_planes_refined	0.003
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_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	2410
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	15

Software

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