4E9Z | pdb_00004e9z

Crystal structure of dehydrosqualene synthase (Crtm) from S. aureus complexed with quinuclidine BPH-651 in the S1 site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZCO	PDB ENTRY 2ZCO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4		0.2M POTASSIUM SODIUM TARTRATE, 20% W/ V PEG 3350, 1MM PPI, 1MM BPH-651 (LIGAND), pH 7.4, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.589	α = 90
b = 80.589	β = 90
c = 91.759	γ = 120

Symmetry
Space Group	P 32 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	CCD	MARMOSAIC 225 mm CCD		2010-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F		APS	21-ID-F

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	2.06	50	99.9	0.073		12.7	21615	21594	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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 2ZCO	2.06	30	2	20746	20373	1093	98.2	0.193	0.191	0.19	0.241	0.24	RANDOM	34

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]
0.37	0.18		0.37		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.173
r_dihedral_angle_4_deg	17.626
r_dihedral_angle_3_deg	15.753
r_scangle_it	6.227
r_dihedral_angle_1_deg	5.794
r_scbond_it	3.948
r_mcangle_it	2.435
r_angle_refined_deg	1.331
r_mcbond_it	1.315
r_chiral_restr	0.115
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2392
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	21

Software

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