6L4H

Crystal structure of human NDRG3 C30S mutant

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.759	α = 90
b = 99.759	β = 90
c = 332.71	γ = 120

Symmetry
Space Group	P 31 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		2018-12-04	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)	Rrim I (All)	Rpim I (All)	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	3.4	50	97.7	0.103	0.111	0.039	6.4	6.6		26798

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.46	97.5		0.732	0.787	0.275	0.826		6.7

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6L4B	3.4	47.824	26570	1332	96.992	0.243	0.2415	0.2774	RANDOM	121.104

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]
-1.134	-0.567		-1.134		3.678

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.621
r_dihedral_angle_3_deg	13.709
r_dihedral_angle_4_deg	13.419
r_dihedral_angle_1_deg	6.677
r_lrange_it	4.888
r_lrange_other	4.888
r_mcangle_it	3.433
r_mcangle_other	3.433
r_scangle_it	2.866
r_scangle_other	2.866
r_angle_other_deg	2.296
r_mcbond_it	1.906
r_mcbond_other	1.906
r_scbond_it	1.627
r_scbond_other	1.627
r_angle_refined_deg	1.246
r_symmetry_xyhbond_nbd_refined	0.284
r_symmetry_nbd_refined	0.248
r_symmetry_nbd_other	0.226
r_nbd_refined	0.225
r_nbd_other	0.221
r_symmetry_xyhbond_nbd_other	0.175
r_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.154
r_symmetry_nbtor_other	0.063
r_chiral_restr	0.046
r_bond_other_d	0.036
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8670
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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