6WFJ

Crystal structures of human E-NPP 1: apo

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6WET	PDB entry 6WET

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
3.3	62.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.951	α = 90
b = 159.687	β = 90
c = 209.245	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		2019-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953731	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	2.5	47.487	99.9	0.041	0.999	15.1	26.1		96772

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	2.5	2.54			0.567	0.65	1.3

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	2.5	47.44	96689	4841	99.851	0.201	0.1994	0.2223	60.345

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]
2.03			1.996		-4.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.684
r_dihedral_angle_1_deg	22.967
r_dihedral_angle_4_deg	17.136
r_dihedral_angle_3_deg	15.13
r_lrange_other	10.14
r_lrange_it	10.137
r_scangle_it	5.505
r_scangle_other	5.505
r_mcangle_it	5.012
r_mcangle_other	5.012
r_scbond_it	3.357
r_scbond_other	3.357
r_mcbond_it	3.091
r_mcbond_other	3.09
r_angle_refined_deg	1.373
r_angle_other_deg	1.218
r_nbd_refined	0.196
r_nbd_other	0.182
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.141
r_metal_ion_refined	0.117
r_ncsr_local_group_1	0.093
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.071
r_symmetry_nbd_refined	0.071
r_symmetry_xyhbond_nbd_other	0.044
r_symmetry_xyhbond_nbd_refined	0.024
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12750
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	311

Software

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