3HLF | pdb_00003hlf

Simvastatin Synthase (LovD), from Aspergillus terreus, S5 mutant, S76A mutant, complex with simvastatin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HLE	PDB entry 3HLE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	20% PEG MME 550, 0.1M HEPES pH 8.0, 0.05 M magnesium chloride, 10 mM dithiothreitol, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3	59.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.47	α = 90
b = 75.066	β = 90
c = 131.819	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 315		2009-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9717	APS	24-ID-C

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	60	97.7	0.067	19.538	4.9	38976	38976		-3	47.3

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	99.6		0.35	3.9	4.9	3906

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3HLE	2	49.51	38902	38902	1964	97.34	0.178	0.178	0.176	0.19	0.209	0.22	RANDOM	32.487

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]
0.3			-0.47		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.108
r_dihedral_angle_3_deg	13.746
r_dihedral_angle_4_deg	12.689
r_dihedral_angle_1_deg	5.679
r_scangle_it	3.025
r_mcangle_it	2.648
r_scbond_it	2.036
r_mcbond_it	1.73
r_angle_refined_deg	1.193
r_angle_other_deg	0.864

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.108
r_dihedral_angle_3_deg	13.746
r_dihedral_angle_4_deg	12.689
r_dihedral_angle_1_deg	5.679
r_scangle_it	3.025
r_mcangle_it	2.648
r_scbond_it	2.036
r_mcbond_it	1.73
r_angle_refined_deg	1.193
r_angle_other_deg	0.864
r_mcbond_other	0.483
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3322
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	31

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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.