2IL4 | pdb_00002il4

Crystal structure of At1g77540-Coenzyme A Complex

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (29% PEG 5000, 0.10 M SODIUM CITRATE, 0.10 M PIPES PH 6.5). CRYSTALS SOAKED 16 HOURS IN WELL SOLUTION SUPPLEMENTED WITH 0.009 M acetyl-Coenzyme. Crystals cryo-protected with fomblin 2500, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.905	α = 90
b = 63.941	β = 90.86
c = 29.525	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	ADSC QUANTUM 315	Double crystal monochromator, Si111, 2nd crystal sagital focus followed by Rh coated bent cylinder vertically focusing mirror	2005-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 8-BM	0.97949	APS	8-BM

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	2.05	31.98	99.2	0.052	18.303	4.3		6473

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	2.05	2.1	98		0.251	4.993	3.9	432

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 1XMT	2.054	31.976	6458	636	99.095	0.166	0.16	0.1647	0.22	0.2238	RANDOM	33.963

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]
0.716		2.045	-0.701		0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.241
r_dihedral_angle_4_deg	16.802
r_dihedral_angle_3_deg	16.084
r_scangle_it	6.514
r_dihedral_angle_1_deg	5.958
r_scbond_it	4.882
r_mcangle_it	2.621
r_angle_refined_deg	1.664
r_mcbond_it	1.608
r_nbtor_refined	0.305
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.163
r_symmetry_vdw_refined	0.163
r_chiral_restr	0.111
r_symmetry_hbond_refined	0.083
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	728
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	48

Software

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