2P8U | pdb_00002p8u

Crystal structure of human 3-hydroxy-3-methylglutaryl CoA synthase I

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FA0	PDB entries 2FA0,2F82,2FA3,2F9A,1XPL
experimental model	PDB	2F82	PDB entries 2FA0,2F82,2FA3,2F9A,1XPL
experimental model	PDB	2FA3	PDB entries 2FA0,2F82,2FA3,2F9A,1XPL
experimental model	PDB	2F9A	PDB entries 2FA0,2F82,2FA3,2F9A,1XPL
experimental model	PDB	1XPL	PDB entries 2FA0,2F82,2FA3,2F9A,1XPL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	297	0.2M (NH4)2SO4, 0.1M Bis-Tris pH 6.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.762	α = 90
b = 92.762	β = 90
c = 235.532	γ = 90

Symmetry
Space Group	P 43 21 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	MARMOSAIC 225 mm CCD		2006-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99999	SLS	X10SA

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	94.4	0.128		5	66668	66668

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	2.07	99.7		0.722		6.1

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 entries 2FA0,2F82,2FA3,2F9A,1XPL	2	50	63108	63108	3380	94.5	0.16149	0.16149	0.15933	0.17	0.20227	0.21	RANDOM	24.337

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			0.22		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.212
r_dihedral_angle_4_deg	17.088
r_dihedral_angle_3_deg	12.14
r_scangle_it	7.182
r_dihedral_angle_1_deg	6.02
r_scbond_it	5.87
r_mcangle_it	3.463
r_mcbond_it	2.52
r_angle_other_deg	1.378
r_angle_refined_deg	1.345
r_mcbond_other	0.654
r_symmetry_vdw_other	0.227
r_nbd_refined	0.205
r_nbd_other	0.192
r_nbtor_refined	0.177
r_symmetry_vdw_refined	0.172
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.142
r_nbtor_other	0.093
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7135
Nucleic Acid Atoms
Solvent Atoms	745
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing