8WTR | pdb_00008wtr

HUMAN SQUALENE SYNTHASE IN COMPLEX WITH (1S,3R)-3-[2-Chloro-5-(2,2-dimethyl-propyl)-13-(2-methoxy-phenyl)-6,8-dioxo-5,6,7,8,10,11-hexahydro-13H-12-oxa-5,9-diaza-benzocycloundecen-9-yl]-cyclohexanecarboxylic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in house x-ray structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG8000/ 50mM KH2PO4/ 1mM DTT. Complex crystal was prepared by soaking in 20% PEG8000/ 50mM KH2PO4, pH 6/ 1mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.33	α = 90
b = 60.016	β = 116.66
c = 85.558	γ = 90

Symmetry
Space Group	C 1 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	IMAGE PLATE	RIGAKU RAXIS VII		2003-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	38.23	99.9	0.074	0.074	7.5	3.53		26854

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		0.235	2.9	3.48

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	25	25539	1294	99.77	0.1664	0.1637	0.16	0.2193	0.22	RANDOM	18.952

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]
0.94		-0.84	0.3		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.096
r_dihedral_angle_4_deg	18.396
r_dihedral_angle_3_deg	13.416
r_dihedral_angle_1_deg	5.301
r_angle_refined_deg	1.623
r_chiral_restr	0.1
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2653
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms	45

Software

Software
Software Name	Purpose
d*TREK	data reduction
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	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.