7C90 | pdb_00007c90

Crystal structure of Cytochrome CL from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT (Ma-CytcL)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D0W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1600 mM sodium/potassium phosphate monobasic, 100 mM HEPES/sodium hydroxide pH 7.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.76	α = 90
b = 76.06	β = 106.85
c = 66.44	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 270		2019-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97941	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.13	50	99.9	0.103	0.111	0.042	11.7	7.2		32914

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.17	100		0.63	0.678	0.248	0.901		7.4

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	2D0W	2.13	30.58	30244	1953	97.42	0.1509	0.1478	0.1575	0.1998	0.2066	RANDOM	37.923

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]
0.21		0.06	-0.42		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.25
r_dihedral_angle_3_deg	16.145
r_dihedral_angle_4_deg	12.28
r_dihedral_angle_1_deg	6.661
r_angle_refined_deg	2.113
r_angle_other_deg	1.365
r_chiral_restr	0.117
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4683
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	266

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing