6WEV

Crystal structures of human E-NPP 1: bound to N-{[1-(6,7-dimethoxy-5,8-dihydroquinazolin-4-yl)piperidin-4-yl]methyl}sulfuric diamide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		281	7.5 mg/mL protein against 19-22% PEG4000, 240-270 mM trilithium/triammonium/tripotassium citrate

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.278	α = 90
b = 158.993	β = 90
c = 209.23	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	PIXEL	DECTRIS EIGER X 16M		2019-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953736	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	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	2.9	47.322	99.9	0.085	0.993	9.9	26		61713

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.98			0.74	0.569	1.1

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	PDB entry 6WET	2.9	47.28	61629	3122	99.893	0.213	0.2112	0.2534	62.639

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]
1.945			4.251		-6.196

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.626
r_dihedral_angle_1_deg	20.716
r_dihedral_angle_4_deg	18.102
r_dihedral_angle_3_deg	16.288
r_lrange_it	11.852
r_lrange_other	11.849
r_mcangle_it	7.04
r_mcangle_other	7.039
r_scangle_it	7.013
r_scangle_other	7.008
r_mcbond_it	4.436
r_mcbond_other	4.436
r_scbond_it	4.381
r_scbond_other	4.346
r_dihedral_angle_other_3_deg	3.466
r_angle_refined_deg	1.458
r_angle_other_deg	1.233
r_symmetry_nbd_refined	0.208
r_nbd_refined	0.207
r_symmetry_nbd_other	0.18
r_nbd_other	0.18
r_nbtor_refined	0.169
r_metal_ion_refined	0.157
r_xyhbond_nbd_refined	0.148
r_ncsr_local_group_1	0.095
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_refined	0.071
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12734
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	278

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing