3MIC | pdb_00003mic

Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound azide obtained by co-crystallization

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	Co-crystallization: 0.1-0.5mM CuSO4, 1.25mM NiCl2, 100mM sodium cacodylate pH=5.5, 40mM sodium azide and 5% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.454	α = 90
b = 68.579	β = 90
c = 81.409	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	RIGAKU RAXIS IV		2008-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

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	2.4	52	99.5	0.111	25.2	5		15128		-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)
	2.42	2.51	99.9		0.59	3.1	5.1	1467

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	2.42	52	14326	759	99.41	0.19912	0.19572	0.19	0.26435	0.26	RANDOM	45.05

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]
0.57			-1.92		1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.845
r_dihedral_angle_4_deg	13.313
r_dihedral_angle_3_deg	13.296
r_dihedral_angle_1_deg	6.272
r_scangle_it	1.364
r_angle_refined_deg	1.072
r_scbond_it	0.935
r_mcangle_it	0.548
r_nbtor_refined	0.303
r_mcbond_it	0.289
r_nbd_refined	0.183
r_symmetry_hbond_refined	0.169
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.074
r_metal_ion_refined	0.051
r_bond_refined_d	0.008
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	215
Heterogen Atoms	29

Software

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