1JDL | pdb_00001jdl

Structure of cytochrome c2 from Rhodospirillum Centenum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C2C	PDB ENTRY 2c2c

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	PEG 6000, potassium phosphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.139	42.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.7	α = 90
b = 59.9	β = 90
c = 65.4	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	298	IMAGE PLATE	RIGAKU RAXIS IIC		1999-10-10	M	SINGLE WAVELENGTH
2	1		IMAGE PLATE	RIGAKU RAXIS IIC		1999-10-12
3	1		IMAGE PLATE	RIGAKU RAXIS IIC		1999-10-15

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200HB	1.5418
2	ROTATING ANODE	RIGAKU RU200	1.5418
3	ROTATING ANODE	RIGAKU RU200	1.5418

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	1.7	20	98.6	0.07	2986	16.9	13248	13248	2		21.9

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)
	1.7	20	88.4		0.32	149	10	1169

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD, MIR,MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2c2c	1.7	20	2	13248	12801	1079	95.4	0.19	0.1931	0.21	0.1907	random	25.2

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]
-0.5	-0.05

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.4
c_improper_angle_d	1.47
c_angle_deg	1.3
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	892
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	43

Software

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