2DGE | pdb_00002dge

Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GDV	PDB ENTRY 1GDV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEGMME550, MES, ZnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.443	α = 82.51
b = 51.843	β = 62.08
c = 53.685	γ = 63.26

Symmetry
Space Group	P 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 315	Si(III)	2004-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

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	1.5	50	88.3	0.04	20.9	2.9	59952	59952

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	1.5	1.55	66.9		0.183

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 (All)	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	PDB ENTRY 1GDV	1.5	31.47	56923	56923	3029	100	0.18767	0.18767	0.18624	0.19	0.21451	0.21	RANDOM	20.187

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]
-0.48	0.27	0.37	0.62	-0.22	-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.853
r_scangle_it	3.305
r_scbond_it	1.989
r_mcangle_it	1.385
r_angle_refined_deg	1.122
r_mcbond_it	0.706
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.097
r_symmetry_hbond_refined	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.853
r_scangle_it	3.305
r_scbond_it	1.989
r_mcangle_it	1.385
r_angle_refined_deg	1.122
r_mcbond_it	0.706
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.097
r_symmetry_hbond_refined	0.081
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3186
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	174

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.