1H29 | pdb_00001h29

Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Structure of the 16-heme Cytochrome c HmcA at 2.5 A resolution and a view of its role in transmembrane electron transfer

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277	EACH CRYSTALLIZATION ASSAY WAS PREPARED BY ADDING 5 UL OF THE PROTEIN SOLUTION (10 MG/ML) TO A DIALYSIS BUTTON WHICH WAS THEN COMPLETELY SOAKED IN THE CRYSTALLIZATION WAS THEN COMPLETELY SOAKED IN THE SOLUTION. AFTER A FEW DAYS AT 4C, SMALL HEXAGONAL BIPYRAMIDS STARTED STARTED TO APPEAR AND REACHED THEIR MAXIMUM SIZE AFTER ONE WEEK. THE BEST CRYOCRYSTALLOGRAPHY CONDITIONS WERE OBTAINED BY SOAKING THESE CRYSTALS IN A CRYSTALLIZATION SOLUTION CONTAINING 7.5% MPD, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.8	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 220.39	α = 90
b = 220.39	β = 90
c = 102.64	γ = 120

Symmetry
Space Group	P 62

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 4r	MIRRORS	2001-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	2.5	25	91.3	0.064	11.9	6.5		89606

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	2.5	2.59	84		0.354	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.51	30	85075	4494	92.1	0.195	0.192	0.258	RANDOM	30.61

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]
1.57	0.79		1.57		-2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.751
r_scangle_it	2.385
r_scbond_it	1.647
r_angle_refined_deg	1.547
r_mcangle_it	0.97
r_mcbond_it	0.515
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.214
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15038
Nucleic Acid Atoms
Solvent Atoms	497
Heterogen Atoms	2752

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling