4KMG

Crystal structure of cytochrome c6B from Synechococcus sp. WH8102

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	2.2 M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.11	α = 90
b = 28.98	β = 92.3
c = 24.68	γ = 90

Symmetry
Space Group	C 1 2 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	RAYONIX MX225HE	mirrors	2012-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

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	1.4	27.95	97.9	0.059	13.8	3.6	14665	14663		-3

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	1.4	1.49	90.1		0.559	2.02	3.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	R-FREE	PDB ENTRY 4EIF	1.4	27.95	13712	13712	950	97.9	0.12398	0.12003	0.18102	RANDOM	15.413

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]
0.56		-0.02	0.29		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.2
r_sphericity_free	22.466
r_dihedral_angle_4_deg	22.019
r_dihedral_angle_3_deg	12.451
r_sphericity_bonded	8.977
r_dihedral_angle_1_deg	5.02
r_rigid_bond_restr	4.309
r_scbond_it	3.152
r_mcangle_it	2.313
r_mcbond_it	1.946
r_mcbond_other	1.942
r_angle_refined_deg	1.769
r_angle_other_deg	0.965
r_chiral_restr	0.116
r_gen_planes_other	0.026
r_gen_planes_refined	0.019
r_bond_refined_d	0.016
r_bond_other_d	0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	643
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	44

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling