3VJ9

Crystal structure of the human squalene synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EZF	PDB ENTRY 1EZF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	20% PEG 2000 MME, 0.01M NiCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.776	α = 90
b = 76.657	β = 90
c = 82.501	γ = 90

Symmetry
Space Group	P 21 21 21

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 210	Vertically Collimating Premirror, Toroidal Focusing Mirror	2008-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.00000	NSRRC	BL13B1

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	1.52	30	99.5	0.045	40.9	8	51413	51144		1	27.4

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	1.52	1.57	99.3		0.509	4.1	8.1	5077

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EZF	1.52	24.7	51082	2598	99.49	0.16284	0.16017	0.21376	RANDOM	25.876

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]
-0.89			0.98		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.606
r_dihedral_angle_4_deg	17.621
r_dihedral_angle_3_deg	13.123
r_scangle_it	5.268
r_dihedral_angle_1_deg	4.883
r_scbond_it	3.547
r_mcangle_it	2.137
r_rigid_bond_restr	1.644
r_angle_refined_deg	1.419
r_mcbond_it	1.312
r_chiral_restr	0.09
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2705
Nucleic Acid Atoms
Solvent Atoms	459
Heterogen Atoms	2

Software

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