3NYK | pdb_00003nyk

The structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7		Protein at 5 mg/ml concentration. 50mM Na-citrate pH 5.7, 20 mM CoCl2, 2.8 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.033	α = 90
b = 50.033	β = 90
c = 98.803	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	291	IMAGE PLATE	MAR scanner 300 mm plate	Max-Flux mirrors (Osmic Inc.)	2010-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.86	43.33	99.2	0.038	14.5	10.3		11749

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.86	1.93	98.6	98.6	0.073	8.8	5.8	1214

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.86	43.33	11154	556	99.42	0.1509	0.14956	0.16	0.17806	0.18	RANDOM	21.21

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]
0.03	0.01		0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.689
r_dihedral_angle_3_deg	17.656
r_dihedral_angle_4_deg	10.415
r_dihedral_angle_1_deg	6.103
r_scangle_it	3.83
r_scbond_it	2.861
r_mcangle_it	1.569
r_angle_other_deg	1.559
r_angle_refined_deg	1.449
r_mcbond_it	1.398
r_symmetry_hbond_refined	0.421
r_mcbond_other	0.235
r_nbd_refined	0.197
r_nbd_other	0.183
r_xyhbond_nbd_refined	0.18
r_symmetry_vdw_refined	0.173
r_nbtor_refined	0.17
r_symmetry_vdw_other	0.149
r_nbtor_other	0.089
r_chiral_restr	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	916
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Patterson	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
Patterson	phasing