2FA3 | pdb_00002fa3

HMG-CoA synthase from Brassica juncea in complex with acetyl-CoA and acetyl-cys117.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F82	PDB Entry: 2F82

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	17% PEG 20K, 0.25M TMAO, 100mM PIPES, 2mM dithiothreitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 61.6	β = 90
c = 411.79	γ = 120

Symmetry
Space Group	P 61 2 2

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	MARRESEARCH		2005-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.978565	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.5	50	97.4	0.113	16.26	7.9		16567

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.66	85.6		0.489	3.1

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: 2F82	2.52	50	15876	15876	848	98.3	0.18135	0.18135	0.17612	0.18	0.28168	0.17	RANDOM	28.532

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]
0.61	0.31		0.61		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.269
r_dihedral_angle_4_deg	22.982
r_dihedral_angle_3_deg	20.458
r_dihedral_angle_1_deg	7.769
r_scangle_it	3.722
r_scbond_it	2.501
r_angle_refined_deg	2.002
r_mcangle_it	1.527
r_mcbond_it	0.899
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.269
r_dihedral_angle_4_deg	22.982
r_dihedral_angle_3_deg	20.458
r_dihedral_angle_1_deg	7.769
r_scangle_it	3.722
r_scbond_it	2.501
r_angle_refined_deg	2.002
r_mcangle_it	1.527
r_mcbond_it	0.899
r_nbtor_refined	0.317
r_nbd_refined	0.258
r_symmetry_vdw_refined	0.223
r_xyhbond_nbd_refined	0.187
r_symmetry_hbond_refined	0.173
r_chiral_restr	0.12
r_bond_refined_d	0.021
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3513
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
NEMO	data reduction
XDS	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.