6WEU | pdb_00006weu

Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-monophosphate

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
3.32	62.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.01	α = 90
b = 160.143	β = 90
c = 209.632	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	2.65	47.613	100	0.055	0.997	12.1	26.9		82015

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	2.65	2.7			0.816	0.508	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 6WET	2.65	47.57	81930	4208	99.962	0.209	0.207	0.21	0.239	0.24	60.145

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]
1.447			3.265		-4.712

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.682
r_dihedral_angle_1_deg	19.328
r_dihedral_angle_4_deg	17.856
r_dihedral_angle_3_deg	15.516
r_lrange_other	10.996
r_lrange_it	10.995
r_scangle_it	6.201
r_scangle_other	6.201
r_mcangle_it	5.723
r_mcangle_other	5.722
r_scbond_it	3.834
r_scbond_other	3.834
r_mcbond_it	3.567
r_mcbond_other	3.566
r_angle_refined_deg	1.356
r_angle_other_deg	1.185
r_metal_ion_refined	0.322
r_nbd_other	0.256
r_nbd_refined	0.197
r_symmetry_nbd_refined	0.193
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.129
r_symmetry_xyhbond_nbd_other	0.112
r_ncsr_local_group_1	0.102
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.055
r_symmetry_xyhbond_nbd_refined	0.03
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	12698
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	258

Software

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