2E7P | pdb_00002e7p

Crystal structure of the holo form of glutaredoxin C1 from populus tremula x tremuloides

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	277	20% PEG6000, 0.1M CITRIC ACID, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.774	α = 90
b = 97.774	β = 90
c = 91.51	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	BRUKER DIP-6040B		2004-10-29	M	SINGLE WAVELENGTH
2	1	x-ray	95	CCD	ADSC QUANTUM 315		2004-11-06	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.7399, 1.7415, 1.6000	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
1,2	2.1	50	100	0.062		11.4		28968			31.7

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	2.1	2.18	100		0.345		11.4

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	24.75	27449	1469	99.89	0.18591	0.18406	0.2	0.22039	0.23	RANDOM	34.617

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]
0.22	0.11		0.22		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.169
r_dihedral_angle_4_deg	20.187
r_dihedral_angle_3_deg	15.974
r_dihedral_angle_1_deg	6.056
r_scangle_it	3.555
r_scbond_it	3.14
r_angle_refined_deg	1.476
r_mcangle_it	1.438
r_mcbond_it	0.899
r_nbtor_refined	0.295

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.169
r_dihedral_angle_4_deg	20.187
r_dihedral_angle_3_deg	15.974
r_dihedral_angle_1_deg	6.056
r_scangle_it	3.555
r_scbond_it	3.14
r_angle_refined_deg	1.476
r_mcangle_it	1.438
r_mcbond_it	0.899
r_nbtor_refined	0.295
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.095
r_bond_refined_d	0.017
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3262
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	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.