3MLK | pdb_00003mlk

Reduced (Cu+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound nitrite

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, 1.25 mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. The crystal was first soaked in 5mM ascorbic acid and then soaked in 300mM NaNO2 (with 5mM ascorbic acid) for 13 hours at RT., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.973	α = 90
b = 69.317	β = 90
c = 81.114	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		2007-11-17	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	3.1	53	99.9	0.081	23.4	7		7468		-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)
	3.1	3.21	99		0.57	2.2	6	715

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	3.1	52.7	7090	344	99.68	0.2187	0.2156	0.2	0.28204	0.26	RANDOM	62.927

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]
-3.51			1.23		2.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.41
r_dihedral_angle_3_deg	16.967
r_dihedral_angle_4_deg	12.888
r_dihedral_angle_1_deg	6.326
r_scangle_it	1.159
r_angle_refined_deg	1.112
r_scbond_it	0.71
r_mcangle_it	0.53
r_nbtor_refined	0.307
r_mcbond_it	0.301
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.125
r_metal_ion_refined	0.09
r_symmetry_hbond_refined	0.081
r_chiral_restr	0.077
r_bond_refined_d	0.009
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	2388
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	8

Software

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