3OMA | pdb_00003oma

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with K362M mutation

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	277	26-28% PEG-400, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K, vapor diffusion, sitting drop

Crystal Properties
Matthews coefficient	Solvent content
4.12	70.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.019	α = 90
b = 131.579	β = 90
c = 176.626	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 300 mm CCD		2008-07-12		SINGLE WEAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	1.0	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.15	50	92	0.059	13.8	5.5		145094

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	2.15	2.23	57.6		0.497		3	9013

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.3	50	122612	126383	3771	97.57	0.1922	0.1914	0.1915	0.219	0.2192	RANDOM	47.1316

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]
-2.46			0.41		2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.688
r_dihedral_angle_4_deg	19.866
r_dihedral_angle_3_deg	14.135
r_dihedral_angle_1_deg	5.653
r_scangle_it	1.931
r_scbond_it	1.317
r_angle_refined_deg	1.185
r_mcangle_it	1.006
r_mcbond_it	0.592
r_nbtor_refined	0.311
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.172
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.117
r_metal_ion_refined	0.107
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12297
Nucleic Acid Atoms
Solvent Atoms	452
Heterogen Atoms	646

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
MD2	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing