3HNI | pdb_00003hni

Crystal structure of the Zn-induced tetramer 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	293	100 mM HEPES, 30% Jeffamine ED-2001, 1.5 mM zinc chloride, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.208	α = 90
b = 87.935	β = 90
c = 152.174	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	CCD	MARMOSAIC 325 mm CCD		2008-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.0000	SSRL	BL9-2

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	2.35	45.74	98.3	0.118	0.118	5.3	3.4	32669	32114

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	2.35	2.48	96		0.55	0.55	1.4	3.4	4497

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2QLA	2.35	45.74	32072	2296	97.82	0.229	0.226	0.23	0.278	0.28	RANDOM	32.045

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]
0.3			-0.54		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.754
r_dihedral_angle_3_deg	19.843
r_dihedral_angle_4_deg	14.913
r_dihedral_angle_1_deg	4.636
r_scangle_it	2.138
r_scbond_it	1.426
r_angle_refined_deg	1.283
r_mcangle_it	0.719
r_mcbond_it	0.384
r_nbtor_refined	0.283
r_symmetry_vdw_refined	0.266
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.091
r_metal_ion_refined	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6544
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	352

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOLREP	phasing