5K67

Designed Artificial Cupredoxins

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	274	2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.72	α = 90
b = 57.72	β = 90
c = 183.46	γ = 90

Symmetry
Space Group	I 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2016-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0000	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.7	45.9	66.9	0.092	1	9.7	5.1		11863

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	1.7	1.73	64.3		1.997	0.7	4.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2QCB	1.7	45.9	11233	589	67.14	0.17488	0.17182	0.23397	RANDOM	23.625

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]
-0.25			-0.25		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.324
r_dihedral_angle_4_deg	19.268
r_dihedral_angle_3_deg	13.143
r_sphericity_free	12.044
r_sphericity_bonded	10.914
r_dihedral_angle_1_deg	7.62
r_scangle_other	6.288
r_long_range_B_other	6.087
r_long_range_B_refined	6.064
r_scbond_it	4.944
r_scbond_other	4.916
r_mcangle_other	4.336
r_rigid_bond_restr	4.328
r_mcangle_it	4.308
r_mcbond_it	3.767
r_mcbond_other	3.593
r_angle_refined_deg	2.523
r_angle_other_deg	1.062
r_chiral_restr	0.125
r_bond_refined_d	0.025
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	924
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing