6W2L | pdb_00006w2l

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X06	1X06, 6JCN
experimental model	PDB	6JCN	1X06, 6JCN

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.22	0.255	0.26	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 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.