2E84 | pdb_00002e84

Crystal structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Miyazaki F) in the presence of zinc ion

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	294	PEG 6000, zinc acetate, pH 6.5, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.09	α = 90
b = 84.07	β = 90
c = 142.67	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	MAR CCD 165 mm		2000-01-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	0.7000	SPring-8	BL44B2

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	2.7	30		0.053	13.3	4.72	20426	20426			33.6

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)
	2.7	2.8	67.6		0.115	3.6		1369

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		THROUGHOUT	2.7	27.2	18096	18096	2006	99.5	0.204	0.204	0.2	0.259	0.25	RANDOM	40.5

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]
-3.38			-2.45		5.83

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	17
c_scangle_it	6.13
c_mcangle_it	4.66
c_scbond_it	4.6
c_mcbond_it	2.95
c_angle_deg	0.9
c_improper_angle_d	0.64
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3813
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	696

Software

Software
Software Name	Purpose
CNS	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing