3GAN | pdb_00003gan

Crystal structure of gene product from Arabidopsis thaliana At3g22680 with bound suramin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VK5	PDB entry 1VK5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		297	Protein solution (10 mg/ml MSE Protein, 0.10 M NaCl, 0.0003 M TCEP, 0.010 M Suramin sodium salt, 0.01 M Hepes pH 7.0) mixed in a 1:1 ratio with the Well solution (1.1 M Sodium chloride, 1% DMSO, 0.10 M BTP pH 7.0). Cryoprotected with 20% Ethylene glycol, 1.8 M Sodium chloride, 1% DMSO, 0.10 M BTP pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.381	α = 90
b = 58.381	β = 90
c = 90.287	γ = 120

Symmetry
Space Group	P 32 2 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	Adjustable focusing mirrors in K-B geometry	2008-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97949	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	50	99.8	0.09	19.77	7.1		12503

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	2.07	98.7		0.458	2.469	6.2	1199

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1VK5	2	50	12465	598	99.521	0.192	0.19	0.2357	0.241	0.261	RANDOM	30.716

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]
0.995	0.498		0.995		-1.493

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.41
r_dihedral_angle_4_deg	24.229
r_dihedral_angle_3_deg	13.381
r_dihedral_angle_1_deg	5.599
r_scangle_it	5.319
r_scbond_it	3.922
r_mcangle_it	2.443
r_angle_refined_deg	2.382
r_mcbond_it	1.393
r_chiral_restr	0.164
r_bond_refined_d	0.024
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	956
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	173

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction