6L4G

Crystal structure of human NDRG3 I171M/S176H mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6L4B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	200 mM ammonium citrate tribasic pH 7.0 and 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.387	α = 90
b = 100.387	β = 90
c = 111.756	γ = 120

Symmetry
Space Group	P 32 2 1

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 PILATUS3 6M		2018-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 11C	0.97942	PAL/PLS	11C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.3	50	99.3	0.164	14	10.5		10073

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.36			0.629

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	6L4B	3.304	47.006	9141	438	90.05	0.198	0.1961	0.2263	33.22

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]
-8.694			-8.694		17.389

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.968
r_dihedral_angle_4_deg	15.386
r_dihedral_angle_3_deg	11.691
r_dihedral_angle_1_deg	6.054
r_lrange_it	5.487
r_lrange_other	5.487
r_mcangle_it	3.282
r_mcangle_other	3.281
r_angle_other_deg	2.319
r_scangle_it	2.305
r_scangle_other	2.305
r_mcbond_it	1.828
r_mcbond_other	1.827
r_angle_refined_deg	1.279
r_scbond_it	1.226
r_scbond_other	1.226
r_nbd_other	0.33
r_symmetry_nbd_refined	0.278
r_symmetry_nbd_other	0.223
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.133
r_symmetry_nbtor_other	0.064
r_chiral_restr	0.047
r_symmetry_xyhbond_nbd_other	0.044
r_bond_other_d	0.036
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4344
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms

Software

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