3HNL

Crystal structure of the Cu-induced dimer of the engineered cyt cb562 variant RIDC-1

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	100 mM HEPES, 200 mM sodium chloride, 25% PEG 3350, 10.7 mM copper sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.165	α = 90
b = 87.045	β = 90
c = 80.765	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	APEX II CCD		2008-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	SIEMENS	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	2.2	22.2	98.7	0.168	0.168	6.5	3.12	12174	12016

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	2.2	2.3	96.5		0.48	0.48	2	1.7	1473

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2QLA	2.2	22.2	12174	11999	832	98.84	0.208	0.208	0.204	0.27	RANDOM	13.357

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]
-0.04			0.08		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.337
r_dihedral_angle_3_deg	19.146
r_dihedral_angle_4_deg	10.924
r_dihedral_angle_1_deg	4.644
r_scangle_it	1.87
r_scbond_it	1.178
r_angle_refined_deg	1.104
r_mcangle_it	0.676
r_mcbond_it	0.373
r_nbtor_refined	0.282
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.075
r_metal_ion_refined	0.02
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1638
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	90

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
SAINT	data reduction
SADABS	data scaling
MOLREP	phasing