2HX7 | pdb_00002hx7

Crystal structure of Cu(II) Azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CSPHQGAGM"

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AZU	PDB entry 4AZU, with residues 112-121 removed

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
2.26	45.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.989	α = 90
b = 65.276	β = 90
c = 97.909	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"	2006-03-08	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	1.54	54.313	96.6	0.051	0.051	9.6	4.3		36537			17.4

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)
	1.54	1.62	86		0.341	0.341	2	4.1	4673

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4AZU, with residues 112-121 removed	1.55	30	36219	1810	97.76	0.147	0.147	0.144	0.15	0.19	0.2	RANDOM	9.984

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]
-0.35			-0.28		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.651
r_dihedral_angle_4_deg	12.939
r_dihedral_angle_3_deg	10.834
r_sphericity_free	8.084
r_dihedral_angle_1_deg	6.365
r_scangle_it	4.206
r_sphericity_bonded	3.249
r_scbond_it	3.209
r_mcangle_it	2.109
r_mcbond_it	1.698
r_angle_refined_deg	1.563
r_rigid_bond_restr	1.561
r_angle_other_deg	0.933
r_mcbond_other	0.618
r_nbd_refined	0.212
r_symmetry_vdw_other	0.198
r_nbd_other	0.195
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.157
r_chiral_restr	0.111
r_symmetry_vdw_refined	0.102
r_nbtor_other	0.087
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_metal_ion_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1904
Nucleic Acid Atoms
Solvent Atoms	470
Heterogen Atoms	2

Software

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