2GCU | pdb_00002gcu

X-Ray Structure of Gene Product from Arabidopsis Thaliana At1g53580

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		297	24% MEPEG 5K, 0.10 M HEPES PH 8.5, 0.050 M MAGNESIUM SULFATE, vapor diffusion, hanging drop, temperature 297K
2	VAPOR DIFFUSION, HANGING DROP		297	25% MEPEG 5K, 0.10 M HEPES PH 8.5, 0.050 M MAGNESIUM SULFATE (PHASING CRYSTAL SOAKED 2 DAYS IN ABOVE WELL SOLUTION PLUS 0.002 M THIMEROSAL), vapor diffusion, hanging drop, temperature 297K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.607	α = 90
b = 64.469	β = 97.83
c = 127.877	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-06-13	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 300 mm CCD	PAIR OF BIMORPH, RHODIUM COATED KIRKPATRICK-BAEZ MIRRORS	2005-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.23984	APS	22-ID
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.98244	APS	23-ID-D

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	1.48	50	94.6	0.075	12.429	5.9		170395

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	1.48	1.51	67.7		0.435	2.818	2.5	8076

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 (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	SAD	THROUGHOUT	1.477	46.127	170375	8539	94.818	0.178	0.17791	0.1765	0.1746	0.2037	0.2037	RANDOM	19.368

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]
-0.001		0.001	0.002		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.78
r_dihedral_angle_3_deg	11.706
r_dihedral_angle_4_deg	8.594
r_dihedral_angle_1_deg	6.186
r_scangle_it	4.22
r_scbond_it	2.762
r_mcangle_it	1.764
r_angle_refined_deg	1.636
r_mcbond_it	1.14
r_nbtor_refined	0.307
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.118
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7422
Nucleic Acid Atoms
Solvent Atoms	1037
Heterogen Atoms	65

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
ARP/wARP	model building