3U8P | pdb_00003u8p

Cytochrome b562 integral fusion with EGFP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	256B	256B, 2WUR
experimental model	PDB	2WUR	256B, 2WUR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.4		0.1 M MES/NAOH, PH 6.4, 200 MM magnesium acetate and 20% (W/V) PEG 8000; for cryoprotection 16% glycerol was added to the reservoir buffer, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.752	α = 90
b = 125.2	β = 90.37
c = 89.255	γ = 90

Symmetry
Space Group	P 1 21 1

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 315	BENT MIRRORS	2010-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	2.75	30	99.3	0.034	0.034	19.9	3.7		36793

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	2.75	2.82	100		0.324	0.324	2.4	3.8

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	256B, 2WUR	2.75	28.94	34888	1882	99.35	0.20317	0.20099	0.2	0.24192	0.24	RANDOM	63.656

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		0.55	2.52		-2.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.596
r_dihedral_angle_3_deg	16.22
r_dihedral_angle_4_deg	13.865
r_dihedral_angle_1_deg	6.25
r_angle_other_deg	4.18
r_scangle_it	2.093
r_angle_refined_deg	1.508
r_scbond_it	1.258
r_mcangle_it	0.899
r_mcbond_it	0.471
r_symmetry_vdw_refined	0.234
r_nbd_other	0.233
r_nbd_refined	0.214
r_symmetry_vdw_other	0.201
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.176
r_symmetry_hbond_refined	0.173
r_nbtor_other	0.118
r_chiral_restr	0.077
r_xyhbond_nbd_other	0.066
r_metal_ion_refined	0.042
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_other_d
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7964
Nucleic Acid Atoms
Solvent Atoms	344
Heterogen Atoms	129

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling