2HX8 | pdb_00002hx8

Crystal structure of Cu(I) Azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CSPHQGAGM", at pH5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HX7	Cu(II) form of the protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	29-31% PEG 4000, 100mM magnesium chloride, 100mM Sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.905	α = 90
b = 65.345	β = 90
c = 97.707	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	93	IMAGE PLATE	RIGAKU RAXIS IV	Osmic "blue"	2006-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.542

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	1.547	54.317	99.8	0.053	0.053	10.2	6.7		33470			16.8

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)
	1.6	1.69	99		0.302	0.302	2.4	6.5	4783

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 (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 Oxidised structure in same crystal form	THROUGHOUT	Cu(II) form of the protein	1.6	54.31	33411	1667	99.66	0.14	0.14	0.138	0.15	0.184	0.19	RANDOM	10.285

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]
			-0.97		0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.254
r_dihedral_angle_1_deg	11.236
r_dihedral_angle_3_deg	10.916
r_dihedral_angle_4_deg	10.045
r_sphericity_free	8.093
r_scangle_it	3.945
r_sphericity_bonded	3.336
r_scbond_it	2.966
r_mcangle_it	1.956
r_mcbond_it	1.595
r_angle_refined_deg	1.543
r_rigid_bond_restr	1.448
r_angle_other_deg	0.925
r_mcbond_other	0.577
r_symmetry_vdw_other	0.22
r_nbd_refined	0.202
r_nbd_other	0.191
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.131
r_symmetry_vdw_refined	0.115
r_chiral_restr	0.102
r_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_metal_ion_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1902
Nucleic Acid Atoms
Solvent Atoms	448
Heterogen Atoms	2

Software

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