7NDX | pdb_00007ndx

Crystal structure of the human HSP40 DNAJB1-CTDs in complex with a peptide of NudC

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AGY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	298	0.1 M of sodium acetate trihydrate and 15% (v/v) of polyethylene glycol 400

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.3	α = 90
b = 128.264	β = 90
c = 135.213	γ = 90

Symmetry
Space Group	I 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	193	PIXEL	DECTRIS PILATUS 2M-F		2020-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.54	46.53	99.9	0.14	0.99	16.5	13		12295

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.54	2.65			0.66

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	3AGY	2.541	46.53	12295	607	99.911	0.235	0.2328	0.24	0.2681	0.26	69.028

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]
-3.914			2.607		1.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.139
r_dihedral_angle_4_deg	21.374
r_dihedral_angle_3_deg	18.674
r_dihedral_angle_1_deg	8.467
r_lrange_it	5.915
r_lrange_other	5.914
r_scangle_it	3.895
r_scangle_other	3.895
r_mcangle_it	3.57
r_mcangle_other	3.568
r_scbond_it	2.4
r_scbond_other	2.399
r_mcbond_it	2.247
r_mcbond_other	2.243
r_angle_refined_deg	1.799
r_angle_other_deg	1.154
r_nbd_refined	0.206
r_nbd_other	0.201
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.173
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.137
r_symmetry_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.065
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1430
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	16

Software

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