6W2L

Crystal structure of human dehydrodolichyl diphosphate synthase (NgBR/DHDDS) in complex with Mg and IPP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	2.5 mM MgCl2, 3.3 mM IPP, 0.1 M Bicine, 10% v/v 2-propanol, 22% PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.67	α = 90
b = 185.67	β = 90
c = 113.351	γ = 120

Symmetry
Space Group	H 3 2

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		2019-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.979	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.306	40	99.2	0.108	0.113	0.032	7.5	12.8		31367

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	94.3		0.877	0.927	0.291	0.826		8.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1X06, 6JCN	2.306	37.916	31367	1611	94.939	0.214	0.2123	0.255	72.717

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]
-1.743	-0.871		-1.743		5.654

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.659
r_dihedral_angle_4_deg	19.542
r_dihedral_angle_3_deg	19.369
r_lrange_it	10.999
r_scangle_it	7.911
r_mcangle_it	6.966
r_dihedral_angle_1_deg	6.088
r_scbond_it	5.353
r_mcbond_it	4.63
r_angle_refined_deg	1.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.659
r_dihedral_angle_4_deg	19.542
r_dihedral_angle_3_deg	19.369
r_lrange_it	10.999
r_scangle_it	7.911
r_mcangle_it	6.966
r_dihedral_angle_1_deg	6.088
r_scbond_it	5.353
r_mcbond_it	4.63
r_angle_refined_deg	1.133
r_nbtor_refined	0.306
r_nbd_refined	0.219
r_symmetry_nbd_refined	0.212
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.131
r_chiral_restr	0.092
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3900
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	29

Software

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

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.