2GI0 | pdb_00002gi0

Crystal structure of Cu(I) Phe114Pro Azurin mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GHZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	25% PEG1500, 100mM MMT buffer, pH4. To generate Cu(I), Cu(II) containing crystals were reduced by soaking in reservoir solution with 10mM ascorbate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.39	α = 90
b = 47.86	β = 90
c = 132.55	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	Osmic 'blue'	2005-10-25	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.551	66.275	94.1	0.065	0.065	6	4.9	24113	24113			18.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.79	85.6	85.6	0.287	0.287	2.4	5.2	3111

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	Direct use of Cu(II) structure in refinement	THROUGHOUT	2GHZ	1.7	47.8	24057	24057	1208	93.97	0.181	0.181	0.179	0.1762	0.224	0.22	RANDOM	16.958

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]
0.55			0.54		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.655
r_dihedral_angle_3_deg	12.283
r_dihedral_angle_1_deg	6.997
r_scangle_it	3.759
r_dihedral_angle_4_deg	3.621
r_scbond_it	2.505
r_mcangle_it	1.573
r_angle_refined_deg	1.528
r_mcbond_it	1.079
r_nbtor_refined	0.299
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.11
r_metal_ion_refined	0.026
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1970
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling