6L4B

Crystal structure of human WT NDRG3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XMQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	200 mM sodium citrate tribasic dehydrate, 20% PEG 3350

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.341	α = 90
b = 100.15	β = 90.01
c = 110.744	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 270		2018-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

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	2.2	50	99.7	0.101	15.9	5.2		95796

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	2.2	2.24			0.641

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	2XMQ	2.2	46.671	88790	4347	92.228	0.169	0.1677	0.1848	31.604

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]
-3.683		-19.234	-5.101		8.784

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.682
r_dihedral_angle_4_deg	15.101
r_dihedral_angle_3_deg	12.791
r_dihedral_angle_1_deg	6.084
r_lrange_it	3.162
r_lrange_other	3.155
r_angle_other_deg	2.3
r_mcangle_it	1.517
r_mcangle_other	1.516
r_angle_refined_deg	1.143
r_mcbond_it	0.828
r_mcbond_other	0.828
r_scangle_it	0.813
r_scangle_other	0.812
r_scbond_it	0.427
r_scbond_other	0.427
r_nbd_other	0.306
r_symmetry_nbd_refined	0.26
r_symmetry_nbd_other	0.198
r_nbd_refined	0.171
r_xyhbond_nbd_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.162
r_nbtor_refined	0.144
r_symmetry_xyhbond_nbd_other	0.084
r_symmetry_nbtor_other	0.062
r_chiral_restr	0.04
r_bond_other_d	0.036
r_gen_planes_refined	0.003
r_gen_planes_other	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13134
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms

Software

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