2HK2

Crystal structure of mevalonate diphosphate decarboxylase from Staphylococcus aureus (monoclinic form)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	0.1M Tris, 1.8M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.495	α = 90
b = 53.061	β = 94.82
c = 100.882	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 4	mirrors	2004-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	46.92	100	0.102	0.102	6.6	5.2	40530	40530	2	2	22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.42	100		0.295	0.295	2.5	5.1	5875

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.3	46.92	40530	40530	2030	99.99	0.194	0.191	0.191	0.249	RANDOM	14.837

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]
0.66		-0.24	-0.82		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.874
r_dihedral_angle_4_deg	26.915
r_dihedral_angle_3_deg	19.824
r_dihedral_angle_1_deg	6.697
r_scangle_it	3.85
r_scbond_it	2.423
r_angle_refined_deg	1.805
r_mcangle_it	1.516
r_mcbond_it	0.915
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.874
r_dihedral_angle_4_deg	26.915
r_dihedral_angle_3_deg	19.824
r_dihedral_angle_1_deg	6.697
r_scangle_it	3.85
r_scbond_it	2.423
r_angle_refined_deg	1.805
r_mcangle_it	1.516
r_mcbond_it	0.915
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.257
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.187
r_chiral_restr	0.133
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5255
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.